Version 2013.4 Rev 1 (2013-04-30 19:09 UTC) ------------------------------------------- * Generate Report: - The Acta Crystallographica C/E report template is now compatible with the atom_site_refinement_flags_adp|occupancy|posn items in XL-2013 CIF files. Version 2013.4 (2013-04-11 20:42 UTC) ------------------------------------- * General: - The Bruker Suite installer no longer allows updating the schema of a remote database server. Only the local installation on the server can update the schema. - A third-party acknowledgements window has been added to the help menu. * Center Crystal: - When driving the Automated Goniometer Head (AGH) with the +/- buttons, the AGH now moves by a single step if the user clicks the button (presses and releases the button in short order). As before, the AGH will move continuously if the user presses and holds the button. * Data Collection Strategy ("Queen"): - On dual source systems, avoid the shadow of the inactive beam stop in the images if possible. - On dual source kappa systems, keep omega scans away from the area between the two collimators and the two beam stops. - Improve strategy for segmented theta ranges, i.e. when 2Theta can not be positioned at zero for very short dx. - Add a security margin to high chi values, as to easily scan below the collimator or the beamstop. - Fix a mistake that applies to X-ray systems with a negative theta range larger than the positive theta range. The extended range on the negative side was not taken into account when calculating the strategy. * Determine Unit Cell: - Added support for the Linux version of CellCheckCSD to APEX2. The path to the ccdc_searcher program must be in the PATH environment variable for APEX2 to find it. The CellCheckCSD software is not provided by Bruker. Contact the Cambridge Crystallographic Data Centre (http://www.ccdc.cam.ac.uk) to register for and download CellCheckCSD. * Reciprocal Lattice Viewer: - No longer crashes during loading of reflections if the mouse moved in exactly the wrong place at exactly the wrong time. - All window elements update correctly when the window is resized. - No longer crashes during loading if the number of group colors in the bn-config.py file was reduced after a prior viewing of data in the Reciprocal Lattice Viewer. - If the group number of a spot harvested exceeds the number of group colors in the bn-config.py file that group number is available and usable. * Space Groups & Statistics: - The observed number of reflections and the theoretical number of reflections in the first resolution shell are now correct. The first bin contained the numbers of the last bin before. * Transform Unit Cell: - The unit cell dropdown list is now updated correctly if the user switches to a different plug-in (e.g. Determine Unit Cell), deletes a unit cell, and returns to Transform Unit Cell. * XRD2 Eval: - The 2theta integration limits are now updated in the user interface if they were adjusted during the integration. And the updated limits are now used when creating raw files. Version 2013.3 -------------- * Structure Solution: - Space group solutions with unit cell reorientations from Intrinsic Phasing are handled correctly now. * XRD2 Eval: - The plug-in is now also available in PROTEUM2 (if a valid license is installed). Version 2013.2 (2013-02-15 16:44 UTC) ------------------------------------- * General: - Archiving a sample to ZIP no longer results in an infinite archive if the ZIP file is located in the sample folder (seen under Windows only). * Center Crystal: - On Kappa goniometers, the Chi angle for manual AGH control has been changed to the vertical microscope angle, which puts Phi underneath the microscope. Note that Chi is limited to a minimum of 30 degrees to prevent icing problems, i.e. instruments with a vertical microscope angle of zero continue to have Phi positioned to the side of the microscope. - The live video now stops when the user switches to another plug-in. * Crystal Faces: - A Python error no longer occurs if the crystal faces entered by the user describe a crystal with a volume exceeding 1000 mm^3. * Data Collection Strategy ("Queen"): - The user interface had a face-lift, including: - Graphs are permanently visible on screen. - A new graph was added, showing distribution of native and cumulative multiplicity. - New LCD type output boxes showing completeness and average multiplicity. - The "More options", "Show graphs" and "Show runs" buttons are removed. - The file modes now have check boxes in stead of radio buttons. - A new "Apply" button was added to refresh calculation after a resolution change. - A new "Restart" button was added to remove information from previous calculations. - The "Anode" field is now always visible, also for single source systems. - New tab "Edit", allowing to display, modify and validate the strategy runs. - Improved checks on reflection files used with "Already measured" and "Measure from file" options. - The default for reflection file type was changed from hkl to raw, as it is more likely to match the reflection axis setup with the current cell. Re-indexed reflection files should match the setup of the selected cell. - The meaning of "Strict efficiency theta limitations" is redefined, as to use the lowest detector 2Theta setting, that covers the requested resolution over the full height of the detector. - Half sphere and full sphere calculations start out from internal template scans to speed up calculations. - Reciprocal lattice viewer: The Unique view initially will omit the missing reflections, if any. The Expanded view initially shows the first two runs only. It is possible to view the reflections contained in the file selected at the "Already measured" option, in the absence of a strategy. - Changes in selected detector distance can dynamically set/unset and disable/enable the strict efficiency theta limitations option, when some hardware positions can not be reached. * Experiment: - The "New Strategy" button is no longer visible if COSMO is not installed. - If the newdarksforallruns configuration variable is set to True, new dark images will be collected for all runs, even if they have the same exposure time. * Scale: - Don't open up files named 's' by default. This could lead to opening up files from matrix runs by accident. - Catch timeout problem in numerical absorption correction caused by locked .prp file. - Update data on the Numerical Absorption Correction page when the formula is changed. - Catch cases in which the connection between the GUI and SADABS is lost. * Space Groups and Statistics: - Switched to XPREP 2013/1. - PROTEUM2 only: When it is time to write the .hkl file, if the transformation matrix is not the unitary diagonal matrix, then change the name of the output .hkl file and warn the user. - There are now two buttons on the Statistics page to update the resolution limits. One button ONLY updates the resolution limits. The other button updates the resolution limits, and then reprocesses the statistics. * Structure Refinement: - Improved support for XL-2013. * Structure Solution: - Added support for XT 2013/1. - Allow non-alphanumeric characters in the .ins filename for XT. * XPRESSO: - The strategy for D8 QUEST and D8 VENTURE instruments with fixed-Chi goniometer is now a bit more conservative to take into account small differences in the PHOTON 100 collision limits due to varying front-to-phosphor distances. Version 2012.12 (2012-11-15 22:52 UTC) -------------------------------------- * General: - Improved restoring of archived samples whose sample name differs from the name of the sample folder. - The pixel dump table now allows the selected region of pixels to be copied to the clipboard. * Determine Unit Cell: - Corrected the label on the exposure time column of the resolution table to seconds/degree. * Diffraction Space Viewer: - The file dialog for importing the run list no longer displays X-ray aperture images. * Experiment: - Inactive Anode operations in the experiment table no longer interfere with validation. * Find a Reflection: - The file dialog for importing the run list no longer displays X-ray aperture images. * Integrate Images: - The background update scaling factor is now working correctly in conjunction with SAINT V8.22A and later versions. In some cases the background update scaling factor did not take or integration aborted with an error. * Precession Images: - The file dialog for importing the run list no longer displays X-ray aperture images. * Reciprocal Lattice Viewer: - The reflection annotation that is displayed when double-clicking a reflection is now showing the correct value for the resolution. * Simple Scans: - The highest resolution at the specified goniometer position is now displayed. Added the resolution table dialog. Both features are in PROTEUM2 only. * Structure Refinement: - The checkCIF report is now generated anew every time the Open Report button is pressed instead of relying on cached reports. - On startup, Olex2 now loads the structure that is to be refined. * XPRESSO: - The minimum exposure time and the exposure time increment were lowered from 5 s/image to 1 s/image. Version 2012.11 --------------- * General: - Importing of P4P files now removes the "Integration of" part from the compound name. * Determine Unit Cell: - Added unit cell searching in the Cambridge Structural Database (CSD) via CellCheckCSD to APEX2. The CellCheckCSD software is not provided by Bruker. Contact the Cambridge Crystallographic Data Centre (http://www.ccdc.cam.ac.uk) to register for and download CellCheckCSD. * Experiment: - The default settings for the Position operation changed. Now they correspond to the "center" position for Kappa goniometers and to the "mount" position for fixed Chi and Eulerian cradle goniometers. * Integrate Images: - Added the Change Output Directory command to the run list context menu. * Structure Solution: - The SHELX instructions are now correctly set up for the Intrinsic Phasing method if this method is already selected at the time the instruction file is loaded. This is the default. Any instructions pertaining to other methods, e.g. Direct Methods, will be removed. - Multiple solutions by the Intrinsic Phasing method are now correctly displayed when the user switches between them. Version 2012.10 (2012-09-19 20:15 UTC) -------------------------------------- * Center Crystal: - The reticule coordinates are now updated when the user starts the video stream. The reticule stayed in the wrong position before if the stream was started after the reticule had been activated. * Data Collection Strategy (new): - The reciprocal lattice view now updates when the slider position changes. * Determine Unit Cell: - The HKL overlay in the Harvest dialog no longer turns on inadvertently. * Experiment: - Runs on fixed Chi goniometers at detector distances shorter than the beam stop distance, i.e. with 2-theta sufficiently off axis, are now validated correctly. This pertains only to D8 QUEST and D8 VENTURE instruments. * Generate Report: - The file dialog for importing the run list no longer displays X-ray aperture images. - The PROTEUM2 HTML report template now displays hh:mm as units for the data collection time and not "hours" as before. * Integrate Images: - Display an error message if an attempt is made to integrate PHOTON 100 data with an out-of-date version of SAINT that does not handle these properly. * Reciprocal Lattice Viewer: - The Incommensurate tool now calculates in-plane vector measurements correctly for non-orthogonal unit cells such as Triclinic. - Exiting the RLATT standalone application no longer hangs indefinitely. * Scale: - The wavelength for calculating the mass absorption coefficient is now determined from the .raw file. - Improved the handling of long file names. - A Python error no longer occurs when this plug-in is opened in SAINTplus. * Structure Solution: - Added the Intrinsic Phasing method (XT). Bruker AXS Executables v2012.10 or higher is required. Version 2012.9 -------------- No changes. Version 2012.8 (not released) ----------------------------- * General: - The resolution circle in the image displays now takes the vertical beam tilt angle into account. * Experiment: - The user is now informed that images will be overwritten if the experiment is resumed at a gap in an existing run, i.e. if an image is missing from a run but more images exist towards the end of the run. * Generate Report: - Position operations in the experiment were erroneuously included in the run list of the APEX2, PROTEUM2, and SMART X2S HTML report templates. This will no longer be the case on new experiments. - New data values were added to the _atom_sites.solution_* items (mixed, notdet, dual, iterative, other). * Integrate Images: - The file dialog for finding runs no longer displays X-ray aperture images. Version 2012.7 -------------- No changes. Version 2012.6 Rev 1 (2012-07-12 15:26:04 UTC) ---------------------------------------------- Corrected a built error in 2012.6. Version 2012.6 (2012-07-10 15:38:52 UTC) ---------------------------------------- * General: - The concept for instruments with manual detector tracks has been changed. The detector distance is now set by physically moving the detector if the instrument is equipped with a length measurement system (D8 VENTURE and D8 QUEST) or by invoking the new Update Distance command from the Instrument menu (e.g. SMART APEX II). The current detector distance is now used anywhere in the software and is automatically updated when the detector distance changes. - The New Sample dialog now prevents the user from entering space characters for the folder name. * Center Crystal: - The live video now stops when the instrument starts collecting data. * Generate Report: - The PROTEUM2 HTML report template now contains the data collection time in hh:mm format instead of fractional hours. * Scale: - Added the missing point groups m2m, 2mm, -4m2, and -6m2. - Display an error message if a .raw file contains different 2Theta angles for the same run. This happens if a run is overwritten with a shorter run and the images past the end of the new run are integrated together with the new images. Version 2012.5 -------------- * General: - Split the archive sample and restore archive features into separate dialogs for dealing with CDs/DVDs and ZIP files. - Fixed a problem under Windows 7 that sometimes caused the application window not to appear. - When the sample notes are invoked, the notes window is now restored if the user minimized it and the window is raised to the front if it is covered. * Auto-Structure: - The chemical formula is now validated and an error message is displayed if an invalid formula was entered. * Describe: - Added support for fractional multiplicities to the chemical formula parser. * Experiment: - Added additional deicing intervals for 15 minutes, 30 minutes, and 1 hour. * Generate Report: - The XCIF report generator has been disabled. The xcif configuration parameter can be set to True to enable the plug-in if needed. * Scale: - Updated to SADABS 2012/1. * Unwarp and convert images: - Added an error message that is displayed if the user attempts to unwarp images that are not spatially distorted. Version 2012.4 Rev 3 (2012-04-26 18:13 UTC) ------------------------------------------- * General: - Added the ToolAlignment application for running the Allied Vision Technologies GigE Vision camera with settings for the steel ball and the half-beam tool. Version 2012.4 Rev 2 (2012-04-24 20:16 UTC) ------------------------------------------- No changes. Version 2012.4 Rev 1 (2012-04-24 18:43 UTC) ------------------------------------------- * Simple Scans: - A Python error no longer occurs when this plug-in is opened in APEX2server or PROTEUM2server. Version 2012.4 (2012-04-02 21:27 UTC) ------------------------------------- * General: - Importing of P4P files from SAINT with invalid numbers for the time decay no longer produce an error. * Auto-Structure: - If the XL, XM, and XS executables are not installed, the plug-in will not be shown. * Center Crystal: - The plug-in now waits up to 5 seconds for the instrument to become idle after the user clicked one of the drive buttons. If the instrument is still not idle after that, the familiar message is displayed to the user. * Compare Unit Cells: - In APEX2, the plug-in has been moved to the Evaluate category. - Switched to a monospaced font for the text output under Windows, just like under Linux. * Determine Unit Cell: - In the Collect dialog, the controls for the exposure time and for the image width are now disabled if the corresponding fields in the matrix runs are set to specific values. Only if those fields are set to Default is the user allowed to override them. * Experiment: - The Thermostat operation now supports commanding the cryostat to a new temperature without ramping. Delete the value in the Rate field or set the value to 0 (zero). Setting the temperaturerampspeed configuration variable to 0 (zero) makes this the default. * Generate Report: - The APEX2 and SMART X2S HTML report templates no longer display an empty hydrogen atom coordinates table if there are no hydrogen atoms in the structure. * Integrate Images: - Improved the performance when displaying a SAINT list file from the run list. * Reciprocal Lattice Viewer: - The direct space unit cell vectors are now displayed correctly. * Simple Scans: - The spatial correction tables are now downloaded and stored in the database when a scan is performed. * Structure Refinement: - If the XL executable is not installed, the plug-in will not be shown. * Structure Solution: - If the XM and XS executables are not installed, the plug-in will not be shown. * Unwarp and convert images: - Added MAR CCD (.mccd) as another output image format. Version 2012.3 (2012-02-28 20:09 UTC) ------------------------------------- * Determine Unit Cell: - The cell volume ESD, like all other ESDs, is now multiplied by the goodness-of-fit to compensate for underestimated variances of the positions of the harvested spots. * Experiment: - The "automatic" option for image correlation now defaults to uncorrelated for the PHOTON 100 detector. * Generate Report: - The Acta Crystallographica C/E report template as well as the APEX2 and the SMART X2S HTML report templates now display the correct number of decimal places on constrained unit cell lengths, e.g. the b and c axes of a cubic cell. - The APEX2 and SMART X2S HTML report templates now display the correct units for the crystal density. * Space Groups & Statistics: - Increased maximum data set size to 10 million reflections (was 4 million). Version 2012.2 (2012-02-10 16:54 UTC) ------------------------------------- * Find a Reflection: - The initial run list that is automatically selected when the plug-in launches no longer contains runs from multiple wavelengths. This is in line with the file dialog for selecting runs manually, which also allows the selection of runs with the same wavelength only. * Unwarp and convert images: - Added the beam tilt to the list of editable image header properties. Version 2011.11-4 (2012-01-12 20:47 UTC) ---------------------------------------- * General: - The image displays no longer cause an error if certain tools, such as the resolution circle tool, are used on active mask images. * Center Crystal: - The left position on D8 QUEST and D8 VENTURE instruments with Kappa goniometer now drives to the negative Kappa angle. This allows the detector to drive in closer and act as background for the video microscope. * Integrate Images: - The integration engine will now run in multithreaded mode if SAINT V8.14B or later is available. * Space Groups & Statistics: - The symmetry operators for the correct space group are now written to the SHELX instruction file if the crystal system and Bravais lattice selected on the Determine Space Group tab disagree. The Bravais lattice has precedence. Version 2011.11-3 (2011-12-09 14:48 UTC) ---------------------------------------- * Center Crystal: - Fixed a memory leak problem with the crystal video, particularly on the medium resolution video microscope at high frame rates. Version 2011.11-2 (2011-12-07 17:40 UTC) ---------------------------------------- * Center Crystal: - The crystal video is now fully zoomed when the stream is started initially. * XRD2 Eval: - Improved the integration algorithm (the lower right corner of a pixel is now calculated correctly before the pixel value is divided into bins). Version 2011.11-1 (2011-11-14 21:29 UTC) ---------------------------------------- * General: - The user can now control if the instrument status dialog should be raised on important messages. The configuration variable that controls this feature is "statuspopup". The instrument status dialog will not be raised if statuspopup is set to False. The default behavior is to raise the instrument status dialog. - Instrument status messages are now displayed in the status bar of the main window as well as in the instrument status dialog. - Changed "CCD Temperature" to "Chip Temperature" in the instrument status dialog. - The keyboard shortcuts for going back and forth between images and runs in the image viewer are working again. The key sequences are Alt-Left and Alt-Right for the previous and next image, Shift-Alt-Left and Shift-Alt-Right for the first and last image, and Alt-Bottom and Alt-Top for the previous and next run. The keyboard focus must not be on a part of the interface that uses the cursor keys itself, e.g. for moving the text cursor. * Data Collection Strategy (new): - The determine strategy dialog no longer resets the crystal to detector distance upon pressing the Enter key. Pressing the Enter key now starts the strategy optimization process instead. - The control for setting the ending time of the experiment is now always in 24 hour mode, regardless of the locale. Hours and minutes can be set, seconds have been removed. * License Manager: - The license manager no longer shows an expiration date for permanent licenses. See release 2009.5 Rev 1. The expiration date was displayed only on the Order tab. The Activate and Import tabs worked as expected. * Precession Images: - Matrix runs are no longer selected by default. * Reciprocal Lattice Viewer: - The default viewing style for the unit cell tool is now set to grid planes. All three planes are now displayed by default. * Scale: - Performing the numerical absorption correction by determining the linear absorption coefficient from the provided formula could sometimes cause a timeout error. This has been corrected. * Space Groups & Statistics: - Changing resolution limits no longer causes timeout errors on large data sets. - Set the Axis scale for resolution vs. % completeness to always be 0-100 in steps of 20%. - Removed the obsolete "Statistics" button. - Fixed a formatting issue in PROTEUM2 that could prevent the space group from being displayed at the end. Version 2011.11 (2011-10-14 12:48 UTC) -------------------------------------- * Scale: - Performing the numerical absorption correction from a .raw file and a .p4p file without prior unit cell determination within the project no longer results in the error message "No unit cell found. Please re-index the unit cell." Version 2011.10 --------------- Does not exist. Version 2011.9 (not released) ----------------------------- * Center Crystal: - The detector is now moved out of the way when driving to the center position on a fixed-Chi goniometer with motorized detector track. * Generate Report: - The enabled/disabled state of the report sections is now preserved after items were changed in the Miscellaneous or other tabs. Version 2011.8 (2011-07-26 13:52 UTC) ------------------------------------- * General: - It is no longer necessary to explicitly leave manual mode or optical mode before interacting with the instrument through APEX2/PROTEUM2. The instrument will be put back in software control mode automatically. * Diffraction Space Viewer: - A Python error no longer occurs if the user tries to increase the number of contours above 24. * Experiment: - If asked to collect new dark images, this is now only done before a run that is collected in its entirety. No new dark will be collected before resuming a partial run. * Unwarp and convert images: - Added the phosphor efficiency to the list of editable image header properties. Version 2011.7 (2011-06-27 19:02 UTC) ------------------------------------- * Generate Report: - The number of runs mentioned in the summary of the SMART X2S report template is now correct for data collected in extended redundancy mode. - Changed the spelling of "Mo-Kalpha-radiation" to "MoKalpha radiation" in the SMART X2S report template. Version 2011.6 (2011-06-10 14:03 UTC) ------------------------------------- * General: - APEX2 and PROTEUM2 now have splash screens. - Nested network shares are now supported under Windows, e.g. if \\server\frames and \\server\frames\guest are both shared. * Auto-Structure: - If the structure is in an enantiomorphic space group and if the structure was inverted, the TITL card in the ShelX instruction file will now indicate this to avoid confusion with the original space group that is also in the TITL card. - The HTAB and CONF instructions are now added before the final refinement. - The list of most disagreeable reflections is now analyzed for reflections that are potentially clipped by the beam stop. Those reflections are omitted. * Experiment: - In the dialog that is presented to the user when images need to be overwritten in the course of resuming an experiment, the detector distance found in the existing image is now displayed without cm-to-grid offset (just like the requested detector distance, which was already displayed without the offset). * Generate Report: - The value of the _diffrn.ambient_temp_esd item can now be changed. The property is available on the Miscellaneous tab. Version 2011.5 (2011-04-29 12:17 UTC) ------------------------------------- * Space Groups and Statistics: - Improved the responsiveness of the plug-in. Version 2011.4-1 (2011-04-13 19:08 UTC) --------------------------------------- * Space Groups and Statistics: - Corrected a problem with triclinic space groups. - The unit cell contents lines in the GUI are no longer duplicated. Version 2011.4 (2011-04-05 18:08 UTC) ------------------------------------- * General: - The region of interest tool in the image displays no longer leaves lines behind as the rectangle is being dragged across the image. - Importing of P4P files from SMART V5.611 now works correctly. * Data Collection Strategy (new): - Phi scans are now generated for the "Generic phi and omega scans" strategy type if the low temperature limitations are active. - The resolution field now enforces the physical limits of the selected wavelength. * Determine Unit Cell: - The triclinic unit cell in the Bravais dialog is now the conventional reduced cell. * Experiment: - Increased the exposure time tolerance for resuming an experiment to 0.0025 from 0.0020. This allows a deviation of up to 0.60 seconds for a 240 second exposure, whereas before the maximum deviation of 0.48 seconds could be insufficient in some cases and lead to a retake of existing images. - Collecting correlated exposures without retakes in case of topped pixels now works correctly. * Generate Report: - The HTML report template for PROTEUM2 is now in the Linux installer. - If the extinction coefficient was removed from a previous refinement, the report will no longer retain the old value. Version 2011.3 (2011-03-02) --------------------------- * General: - Archive Sample to CD is now compatible with cdrecord in newer Linux distributions. * Center Crystal: - The dialog informing the user that the instrument is not idle is now displayed on top of the Phi 90 and Phi 180 buttons, whichever was pushed, instead of centered on the screen. This prevents the dialog from hiding underneath the Video application which the user may have put in the center of the screen. * Experiment: - If asked to collect new dark images, this is now done only once for each exposure time used in the run list. Subsequent runs with the same exposure time will not take new darks. - The user is now asked for confirmation before executing/resuming an experiment while the instrument is still busy running another experiment. * Scale: - "Finish" button disabled when starting over after running using the numerical absorption correction with the formula. - Problems with the x-axis on the Refinement Graph fixed. - Improvements to the scale factors graphs. No longer have white overdraws, better scaling of the results so that the range isn't clipped. - Fix the chart file reading so that the maximum resolution, redundancy and linear absorption correction are displayed when the plug-in is re-opened. - Reset the linear absorption correction if the plug-in is restarted. - Display the linear absorption correction if the automatic method is used to determine the value. - Prevent extraneous Spatial Distribution tabs if the user switches back and forth between plug-ins. - Improve the display of the Spatial Distribution diagrams. - Limit the number of refinement cycles to 500. Validate the refinement cycles in the GUI. * Space Groups and Statistics: - Numbers and minor tick marks removed from the Lattice Exceptions graph. - Improved the on-line documentation for the Lattice Exceptions graph. - Report back the values of N (total) and N (int > 3 sigma) as integers rather than floats. - Change from a radio button to a checkbox to choose another space group. - Go back to the beginning if there is a lattice exception. - End xprep-t.exe at the interface level if the lattice type cannot be determined. - Remove the extraneous output .hkl file widget when PROTEUM2 is the product. - Re-format the unit cell parameters (to 2 decimal places, rather than 5) - Fix some problems with use of output .sca files. - Linux: Remove an unprintable character from the end of the chart on the Unit Cell Contents page. - Fix the automatic finish parameters with APEX2. - Automatically merge the statistics if the data sets are changed. * X-Presso: - The run list in the Experiment plug-in is no longer changed when an existing data set is processed. Version 2011.2-3 (2011-03-10 14:33 UTC) --------------------------------------- * General: - Eliminated the warning message "This program might not have installed correctly" when installing Bruker Suite under Windows 7. Version 2011.2-2 ---------------- No changes. Version 2011.2-1 (2011-03-01 18:30 UTC) --------------------------------------- * Space Groups and Statistics: - A Python error no longer occurs when the plug-in is running within the SHELXTL product. Version 2011.2 (2011-02-10 20:46 UTC) ------------------------------------- * Data Collection Strategy (new): - A Python error no longer occurs if the resolution limit is set so low that not a single reflection is predicted. * Scale: - The spatial distribution of outliers plots are now displayed without clipping them. - Timeout errors caught, the user is advised to check the CPU usage, and the plug-in goes to the beginning. Version 2011.1 -------------- No changes. Version 2010.13-2 (2011-01-18 15:32 UTC) ---------------------------------------- * General: - The goniometer position is now read correctly from ADSC images if the image header does not indicate the scan axis. Phi is assumed as scan axis in this case. * Crystal Faces: - The angle indicator now works correctly after loading a video zip stream. * Generate Report: - This plug-in is now also available in PROTEUM2. - Added the HTML report template for PROTEUM2. - Increased the number of significant digits for the crystal dimensions in the APEX2 HTML report template to 3 (from 2). - The absolute structure parameter is now displayed in the APEX2 HTML report if its value is zero. - The run list now imports correctly under Windows if the images are located in the root directory of the drive, e.g. D:\. * Integrate Images: - The spot profile is now properly centered in the bounding box if the profile grid is larger than 9x9x9. * Space Groups and Statistics: - In PROTEUM2 this plug-in no longer asks for the chemical formula or protein sequence and a .ins file is no longer generated at the end. Version 2010.13-1 ----------------- Does not exist. Version 2010.13 --------------- Does not exist. Version 2010.12 (2010-11-09 16:34 UTC) -------------------------------------- * Data Collection Strategy (new): - The table in the "Show runs" dialog can now be scrolled up and down. * Find a Reflection: - The detector distance error is now taken into account. Version 2010.11 (2010-10-26 18:24 UTC) -------------------------------------- * General: - P4P files that are exported from APEX2 or PROTEUM2 now use the correct line separator under Windows, i.e. they display correctly in editors that do not support UNIX style line separators (such as Notepad). - Corrected a rare problem with missing icons in APEX2 and PROTEUM2 under Windows. * Data Collection Strategy (new): - The list of unit cells is now updated after importing a P4P file. * Experiment: - Added the Pause operation. * Generate Report: - For atoms on special positions, the SMART X2S report template no longer prints standard uncertainties for the constrained atomic coordinates and anisotropic displacement parameters. * Integrate Images: - Fixed synchronization in the spot position overlay. * License Manager: - The license manager now works under Windows 7. The user must run the license manager with administrative privileges (select "Run as administrator" from the icon context menu under Windows 7). This is regardless of whether the user is already logged in as an administrator or not. * Simple Scans: - Ask to reconnect to the instrument if the user tries to switch anodes while no instrument is connected. * Structure Refinement: - The file dialog for SHELX result files now shows the .re0, .re1, etc. files created by XSHELL. * X-Presso: - Fixed a problem where the resolution limit in the data was sometimes overestimated. Version 2010.10 (2010-09-16 12:18 UTC) released as 2010.9 Rev 1 --------------------------------------------------------------- * Auto-Structure: - Auto-Structure no longer reverts back to a previous structure model that has the wrong handedness as indicated by XL. Version 2010.9 (2010-08-24 14:27 UTC) ------------------------------------- * Auto-Structure: - A Python error no longer occurs if the PLATON CIF check report is missing. * Data Collection Strategy (new): - Corrected a problem in the way the suggested detector distance is calculated. * Diffraction Space Viewer: - The initial view of the reciprocal space is now fully zoomed out. * Scale: - The list of individual batches no longer contains duplicate raw files after switching between plug-ins. * X-Presso: - New plug-in for automated data collection and structure determination. Version 2010.8 (2010-07-24 22:37 UTC) ------------------------------------- * Experiment: - Changed the label of the "Attenuate if topped" checkbox to "Retake if topped." The retake option is now available for uncorrelated as well as for correlated images. - Thermostat commands are now flagged with an error if the connected instrument does not have a thermostat. The thermostat commands are normally not available under these circumstances. But it is possible to import from file an experiment that does contain thermostat commands. * Reciprocal Lattice Viewer: - The reflection list and the unit cell parameters box no longer disappear when the project is saved after reflections have been deleted. * Space Groups and Statistics: - The statistics of systematic absence exceptions sometimes contained incorrect data. Version 2010.7 (2010-06-25 15:59 UTC) ------------------------------------- * General: - The maximum number of images for rendering the rocking curve in the image displays can now be changed with the rockingimagesmax configuration variable. The total number of images used is 2*rockingimagesmax+1. The default value is 15, which covers a range of 31 images. * Center Crystal: - When driving the Automated Goniometer Head (AGH) with the +/- buttons, the AGH now stops driving if the user presses the right mouse button. Before, the AGH would keep driving although the GUI indicated that it had stopped. * Crystal Faces: - The color of the crystal face normals can now be changed by setting the faceindexnormal color configuration variable. The default color is "yellow". * Determine Unit Cell: - The crystal mosaicity used by the overlay of the image display is now updated when reflections are harvested and the mosaicity is determined. * Generate Report: - Symmetry codes imported from a CIF file are now interpreted correctly if the translation symbol is not a digit. For example "1_:55" is now correctly intepreted as a tanslation of +5 asymmetric units along the a axis. - The APEX2 HTML report template now correctly shows the anisotropic atomic dispacement parameters table if the structure in its entirety is located on a special position. * Space Groups and Statistics: - Fixed a Python error that occurred if the space group was not determined. Version 2010.6 (2010-06-07 18:22 UTC) ------------------------------------- * General: - When logging out of the database, the user is now given a cancel option and stay connected to the database. * Scale: - The scale for the mean weight axis in the parameter refinement plot now has a fixed range from 0 to 1. As a result, small changes in the mean weight are no longer inflated to large differences on the screen. Version 2010.5 (2010-05-05 19:37 UTC) ------------------------------------- * Data Collection Strategy (new): - Increased the lower kappa limit for low temperature data collections from 15 degrees to 30 degrees. * Integrate Images: - The Refinement Options dialog now shows the correct inter-component constraints. - The software now warns the user if output files from the integration of a twinned crystal (.mul files) will be overwritten before starting the integration. Before, the software checked only for output files from non-twinned integrations (.raw files). * Generate Report: - Lines in Acta Crystallographica C/E reports could in rare cases get word wrapped in a way that violated the CIF standard. Version 2010.4 (2010-04-02 16:38 UTC) ------------------------------------- * General: - The same restrictions for naming new samples are now enforced also for naming samples that are restored from an archive. Only letters (lower and upper case), digits, and underscores ("_") are permitted. - Archiving a large number of files to DVD is now handled more efficiently. * Center Crystal: - The automated loop centering now stops as expected when the user cancels the centering process. * Reciprocal Lattice Viewer: - The number of reflections in each group is now displayed. * Generate Report: - The number of significant digits for the crystal size has been changed from 2 to 3 in the Acta Crystallographica C/E report template. Version 2010.3 (2010-03-05 20:54 UTC) ------------------------------------- * General: - The user is now informed if archiving a sample to a ZIP file would exceed the maximum archive size, i.e. maximum number of files or bytes. * Auto-Structure: - The anisotropic atomic displacement parameters are now displayed correctly. * Determine Unit Cell: - Images with short exposure times (less than 4 seconds) were collected as uncorrelated images even though the user indicated correlation. * Generate Report: - Removed the deprecated _diffrn_radiation_source item from the Acta Crystallographica C/E report template. Added the _diffrn_source and _diffrn_source_type items. * Integrate Images: - A Python error no longer occurs in the SAINTplus application if no matrix files are specified for integration. * Reciprocal Lattice Viewer: - The Miller indices for the reflections are now calculated for the selected unit cell. * Structure Solution: - File system paths containing periods (".") are now handled correctly by the SHELXTL application. Version 2010.2 (2010-02-05 18:53 UTC) ------------------------------------- * General: - Fixed a Python error that occurred when restoring an archived sample if no CD/DVD drive was configured. - Fixed a Python error that occurred when a sample name that was already in use by another user was entered for restoring an archived sample and the current user did not have access to the other user's sample. * Crystal Faces: - The plug-in has been removed from PROTEUM2. * Describe: - In PROTEUM2, added input fields for the biological source and the sequence of the sample, as well as the crystallization conditions. Removed the chemical formula and simplified the way the crystal color is specified. * Determine Unit Cell: - In PROTEUM2, the plug-in has been moved to the Screen category. * Determine Unit Cell using Phi/Chi: - In PROTEUM2, the plug-in has been moved to the Screen category. * Experiment: - Crystal Video operations are no longer executed when resuming the experiment if no scan needs to be performed. * Generate Report: - Added support for non-ASCII characters, e.g. in the author name or mailing address. Only characters that are compatible with the CIF markup convention are supported. - PCF files from XPREP can now be imported from the Miscellaneous tab. * Integrate Images: - Within the APEX2 and PROTEUM2 applications, the Refinement Options dialog now displays the inter-component constraints only for components that actually exist. * Reciprocal Lattice Viewer: - In PROTEUM2, the plug-in has been moved to the Screen category. * Scale: - The SADABS plots are now correctly generated if ImageMagick is installed in the Program Files directory. * Simple Scans: - In PROTEUM2, the plug-in has been moved to the Screen category, preset goniometer positions have been removed (except user defined goniometer positions), and the preset scans have been modified. * Transform Unit Cell: - The plug-in has been removed from PROTEUM2. * View Images: - In PROTEUM2, the plug-in has been moved to the Screen category. * View Molecule: - The plug-in has been removed from PROTEUM2. Version 2010.1 (2010-01-08 20:34 UTC) ------------------------------------- * Generate Report: - The reports generated from the Acta Crystallographica C/E report template now apply the same threshold for determining the number of significant digits to display as is used in SHELX CIF files. For example, 100.08 +/- 0.19 is now reported as 100.08(19) and not as 100.1(2) as before. Version 2009.12 (2009-11-16 19:51 UTC) -------------------------------------- * General: - Prohibited commas in the sample folder path. The comma causes problems for SAINT and prevents data integration. * Data Collection Strategy (new): - The user can now specify the resolution limit in Angstroms, 1/Angstroms, and in degrees of 2Theta. * Determine Unit Cell: - Fixed a Python error that occurred if the detector distance was reduced to a point where the configured matrix runs were no longer valid. * Experiment: - Added the option to collect spatially unwarped images. * Generate Report: - The report templates now correctly support structures whose atoms are exclusively located on special positions. Version 2009.11 (2009-10-26 15:28 UTC) -------------------------------------- * General: - The alternative sample name that is suggested if a new sample is created while another sample with the same name already exists in the database, now handles names correctly that contain an underscore, followed by a number, followed by non-numeric characters. - The Import > P4P/SPIN File dialog now imports the crystal shape. * Auto-Structure: - Fixed a Python error that occurred if not a single atom was found during structure solution. * Determine Unit Cell: - The estimation of the mosaicity can now be disabled by setting the estimatemosaicity configuration variable to False. This also disables the estimation of the integration box size for the Integrate Images plug-in. * Diffraction Space Viewer: - The initial view of the reciprocal space is now fully zoomed out. The intensity sliders and the 2D cross-section work again. * Experiment: - Added the new "automatic" option for the image correlation. The automatic option chooses single or double correlated images depending on the exposure time. The automatic option is the new default. To switch back to the previous default of double correlated images, set the numimg configuration variable to 2. * Simple Scans: - The Chi axis controls are no longer available on instruments with a fixed-Chi goniostat. * Structure Refinement: - Added a button for launching Olex2. The button is visible only if Olex2 is installed. * View Molecule: - The anisotropic atomic displacement parameters are now displayed correctly. Version 2009.10 (2009-09-23 18:17 UTC) -------------------------------------- * General: - The generator voltage (kV) in the instrument status dialog is now displayed without decimals. - The frame rate slider in the image displays now works. * Auto-Structure: - Fixed a Python error that occurred in some cases if the structure solution had failed. * Generate Report: - The Acta Crystallographica C/E report template now works correctly with a Flack parameter of zero. - The Acta Crystallographica C/E report template now uses the _space_group_* items instead of the superseded _symmetry_* items. * Precession Images: - The computation of precession images is back at its original speed. In releases 2009.7 and 2009.9 the calculation was very slow. Version 2009.9 (2009-08-28 22:12 UTC) ------------------------------------- * Crystal Screening: - The crystal screening software can connect to BIS again. * Experiment: - When an experiment is resumed, non-scan operations such as a Thermostat Off are now executed even if they are not followed by a scan operation. - When images need to be overwritten in the course of resuming an experiment, the user is now presented with the reasons why the images need to be retaken. * Integrate Images: - The application no longer locks up at the end of the integration, as had been observed on a small number of installations. * Scale: - The specified raw files are now processed in the correct order under Linux. - The Numerical Absorption Correction may now be done with unmerged files as well as merged files. - The correct name is now given to the .abs file. * Space Groups and Statistics - When a protein sequence is converted to a formula, the radio button marked "Chemical Formula" is checked. Version 2009.8 (2009-07-30 13:24 UTC) ------------------------------------- * General: - Added the Import All check box to the Import > P4P/SPIN File dialog. - The requested exposure time displayed in the image viewer header display is now correct if the image was correlated from individual exposures of varying exposure times. * Generate Report: - The template list now comes populated with the available report templates. The browse button next to the template list has been replaced with a browse entry in the template list. - Added the _chemical_absolute_configuration item to the Acta Crystallographica C/E report template. Note that the item will be missing if the Hall symbol indicates a non-chiral space group. - Removed leading whitespace from the value of the _symmetry_space_group_name_Hall item in the Acta Crystallographica C/E report template. These whitespace characters caused problems with checkCIF. * Integrate Images: - The q-vector refinement parameters are now available in the Refinement Options dialog. - The semi-transparent bounding box in the spot profile display is back. Version 2009.7 (2009-07-07 12:10 UTC) ------------------------------------- * General: - The maximum auto-rotation speed of the molecule in the structure viewers has been limited to approximately 2 RPS. When the structure viewer is in Z rotation mode, the auto-rotation now spins the molecule around Z as well. - Restoring multiple samples from CD/DVD in a row no longer results in an error. * Auto-Structure: - Noble gases are now allowed in chemical structures. Neptunium (Np) is now allowed in chemical structures. * Determine Unit Cell: - Eliminated much of the delay encountered when specifying the images to use for harvesting (name of first image, number of runs, number of images per run). * Experiment: - Runs on instruments with AXIOM detectors were sometimes not collected in fastscan mode or shutterless mode. * Generate Report: - The run list no longer changes in reports generated from the SMART X2S report template if the data set is reprocessed in APEX2 and the crystal symmetry changes from triclinic to non-triclinic or vice versa. * Scale: - Fixed a problem which was causing an infinite loop when a .p4p file was read in for use of the Numerical Absorption Correction using XPrep with a modulated structure. * Structure Refinement: - The structure viewer now clears an old structure before a new structure is loaded. - The plug-in is now smarter about deciding which .ins/.res file to load upon startup. * Structure Solution: - The application no longer hangs if it finds an incomplete .lst when the plug-in is launched. Version 2009.6 (2009-06-03 18:23 UTC) ------------------------------------- * Generate Report: - Newline characters are no longer removed from *_details items in the Acta Crystallographica C/E report template. Version 2009.5 Rev 1 (2009-05-22 14:52 UTC) ------------------------------------------- * Scale: - .abs files starting with an 'F' are no longer permitted. If the file is on the 'F' drive, then we use the local name. If the local name starts with an 'F', we use sad.abs. * Experiment: - Images collected with an APEX DUO could sometimes have the wrong anode name prepended to the file names. - Operations are no longer lost if the user is in the process of editing an operation and then loads an experiment or switches to a different plug-in. * License Manager: - An expiration date is no longer displayed for permanent licenses. Version 2009.5 (2009-05-08 18:42 UTC) ------------------------------------- * General: - In the structure viewers the molecule is now rotating in the correct direction when the user drags the mouse cursor across the view with the left mouse button held down. - A Python error no longer occurs if multiple samples are simultaneously archived to XML files from different APEX2 or PROTEUM2 applications. * Auto-Structure: - Auto-Structure is now enabled by default in APEX2 and in SHELXTL. A separate license is no longer needed. * Determine Unit Cell: - Deleting a group of reflections that was created in the Reciprocal Lattice Viewer now works correctly. * Generate Report: - Hydrogen bonds without esds are now shown in the Acta Crystallographica C/E report and in the HTML report. * Integrate Images: - Inter-component constraints work again. These constraints were not applied since version 2008.6 when the inter-component defaults were changed so that twin domains were supposed to always share the same unit cell parameters. This failed with SAINT V7.65A and older. * Reciprocal Lattice Viewer: - A Python error no longer occurs if the user deleted the images used for the unit cell determination and then exports the visible spots to a P4P file. * Structure Refinement: - The correct PLATON report is now used for the Generate Report plug-in. The .fck report was used before instead of the .chk report. Version 2009.4 (2009-04-08 15:06 UTC) ------------------------------------- * General: - Archiving to CD-R(W) and DVD+/-R(W) is now possible with Microsoft's Image Mastering API v2.0 (IMAPIv2.0). This is an alternative to Cdrtools under Windows and supports some writers that Cdrtools does not support. The Image Mastering API for Windows XP can be downloaded from this location: http://support.microsoft.com/kb/932716. Windows XP with Service Pack 2 or 3 is required to install IMAPIv2.0. Once it is installed, APEX2 and PROTEUM2 will use the Image Mastering API in favor of Cdrtools. APEX2 and PROTEUM2 can be instructed to still use Cdrtools by setting the useimapi2 configuration variable to False. - Corrected a number of problems with restoring archived samples from ZIP files and from CDs. * Auto-Structure: - A Python error that occurred when the plug-in was running in the SHELXTL standalone application has been fixed. * Crystal Faces: - The T-tool no longer becomes visible when a context menu command is invoked if the user has hidden the T-tool. Previously, it was not possible to save a JPEG without the T-tool visible in the image. * Data Collection Strategy: - In the dialog for generating axial runs, the OK button has been relabeled to Add Run. * Generate Report: - The _exptl_absorpt_correction_T_min and _exptl_absorpt_correction_T_max items in the Acta Crystallographica C/E report template are now rounded to two significant digits. - Added the _chemical_formula.moiety and _refine.details items to the Miscellaneous tab. Version 2009.3 (2009-03-12 14:30 UTC) ------------------------------------- * General: - The image displays now inform the user when an image is loaded that was collected at a different wavelength than is associated with the unit cell and instrument parameters in the database, if the new "trustimageheader" configuration variable is set to False. The new default behavior is always to accept the wavelength from the image header. This feature is intended for synchrotron users. * Scale: - Rearranged the GUI to improve ease of use. * Determine Unit Cell: - Bravais lattice type "Rhombohedral R" is now available in the unit cell editor dialog. * Experiment: - Some runs were flagged as invalid when their direction was determined automatically on an APEX DUO if those runs would have been collected with the anode that was inactive at the time of validation. * Generate Report: - Removed the _diffrn_standards_* items from the Acta Crystallographica C/E report template. * Integrate Images: - A Python error no longer occurs if an integration results in huge deviations (hundreds of pixels) between observed and predicted reflection positions. * Reciprocal Lattice Viewer: - A Python error no longer occurs if the user adds angles or distances without first measuring them. * Structure Refinement: - There is now a button marked 'Open Report'. If there is a .cif file, clicking on this button creates and displays a Platon file. The Platon file is now put into the audit trail as well. Version 2009.2 (2009-02-11 18:45 UTC) ------------------------------------- * General: - Added the Reopen submenu to the Sample menu. - Added the Run command to the Sample menu. - The image displays now inform the user when an image is loaded that was collected at a different wavelength than is associated with the unit cell and instrument parameters in the database. The user is given the choice either to use the wavelength from the image or from the database. This feature is intended primarily for APEX DUO systems. - When a P4P file from CELL_NOW is imported, the Bravais lattice type in the P4P file is now ignored. CELL_NOW does not determine the symmetry of the unit cell it finds and whatever symmetry information is stored in the P4P file was simply copied by CELL_NOW from its input P4P file. * Center Crystal: - Changed the orientation of Phi for the left, right, and mount positions so that the screw for adjusting the height on a Huber goniometer head is in a more convenient position. * Data Collection Strategy: - Added a new feature for generating axial runs. The new commands are accessible from the menu bar. Axial runs can be generated for reciprocal unit cell axes and for even rotation axes of the crystal's Laue class. The axial runs can be combined with runs from the hardware profile, allowing the user to refine a data collection strategy by filling in gaps in the reciprocal space coverage of the axial runs. - Added a new refinement target called redundancy evenness. The redundancy evenness attempts to equalize the dataset redundancies across resolution shells. Note that evening out the redundancy distribution generally requires a larger number of runs and is more effective for higher resolution limits where a larger number of runs is required. Also note that COSMO in version 1.59 or later is needed to use this feature. - Parameter priorities are now restored next time the plug-in opens, even if the priorities are zero. - Hardware profiles in Kappa geometry are now converted to Eulerian geometry on the fly and no error is displayed as before. Because of the delay caused by the conversion it is still recommended to use an already converted hardware profile. * Determine Unit Cell: - If the user decides not to continue harvesting spots when the software finds fewer images for indexing than specified, the automatic mode no longer proceeds to indexing (which it did previously if there were spots available from an earlier harvest operation). * Determine Unit Cell using Phi/Chi: - A Python error no longer occurs if the user clicks the Harvest button while the "phichi" folder in the sample directory is empty. * Experiment: - Added support for deicing. The user has the choice between deicing every 1, 2, or 5 minutes or not deicing at all. - The default values for the exposure time, image width, image correlation, and deicing interval are now user configurable. Five new configuration variables have been introduced: * frametime - exposure time in seconds per image (default: 10.0) * degreetime - exposure time in seconds per degree (default: None) * frameangle - image width in degrees (default: 0.5) * numimg - number of exposures to correlate (default: 2) * deicetime - deicing interval in seconds (default: None) If frametime and degreetime are both configured, degreetime wins. - When images need to be overwritten in the course of resuming an experiment, the user is now presented with the reasons why the images need to be retaken. - The maximum allowed deviation between the requested exposure time and the found exposure time when resuming an experiment can now be configured by specifying the relative exposure time tolerance in the configuration variable exposuretimetolerance. The default for exposuretimetolerance is 0.002 (0.2%). * Generate Report: - The molecule viewer in the HTML report template can now display thermal ellipsoids. - The HTML report template now shows standard uncertainties for atom coordinates of hydrogen atoms that were freely refined. * Integrate Images: - In the Integration Options dialog it is now possible to specify the number of Monte Carlo simulations to run. Note that SAINT V7.53A or later is needed for this feature. - Removed the controls for the Multiwire reference correction from the Integration Options dialog. - The default settings for the SAINT+ Integration Engine can now be changed without losing these changes each time the software is updated. To do this, a customized saint.ini file must be placed in the root of the Windows system drive, e.g. C:, or in /usr/local/lib for Linux systems. Per-user settings can in addition be put in %USERPROFILE%\saint.ini for Windows and ~/.saint for Linux. - The temporary .ini, .p4p, and .slm files are now truly temporary and are deleted after the integration finished. If these files should not be removed, the user should check the Keep Temporary Files check box in the Integration Options dialog. - In the Find Runs dialog it is no longer possible to select runs that were collected at different wavelengths. If there are already runs in the run list, only runs collected at the same wavelength can be added with the Find Runs dialog. * Simple Scans: - The "Current" button works again. - The Still and Phi 360 scans were sometimes considered invalid even if the goniometer position was accessible. - When the anode is switched on an APEX DUO, the active anode is now updated in the Simple Scans plug-ins of all applications that are connected to the instrument. Version 2009.1 (2009-01-16 19:33 UTC) ------------------------------------- * General: - The user's database login name is now sent to the Bruker Instrument Service whenever a connection to the instrument is established. This feature allows BIS to track instrument usage by user. Note that if no user is logged in, the name of the operating system user will be sent instead. - When a P4P file from CELL_NOW with more than four unit cells is imported, the domain assignment for reflections belonging to the first four unit cells will no longer be lost. Unassigned reflections and reflections belonging to unit cells five and higher will be put in a separate group. * Scale: - The numerical absorption correction has been changed to use SADABS instead of XPREP. * Crystal Faces: - The real space or reciprocal space unit cell axes or the goniometer axes can now be displayed. - Pressing the CTRL key will now constrain the T-tool to its current direction for as long as the CTRL key remains pressed. This makes measuring of crystal faces close to the center easier because the user can now snap the T-tool to the desired direction, press the CTRL key, and move as close to the center as necessary without losing the direction of the T-tool. - The length of the "horizontal" line of the T-tool is now limited to a minimum of half the image height. This makes measuring of crystal faces close to the center easier. - Improved the placement of crystal face labels. - Added the "Flip 90 degrees" command to the context menu. * Determine Unit Cell: - Improved the performance of the harvesting algorithm. Note that Python environment v6.2 or later is needed to benefit from this improvement. - The reflection list editor can now copy reflections to the clipboard so that they may be imported into a spreadsheet. - A Python error no longer occurs if the last unit cell is deleted. * Experiment: - Added a new operation for acquiring crystal videos for face indexing. - Possible omega ranges are now displayed with their total width in addition to their starting and ending angles. * Simple Scans: - Added a dedicated button for switching the anode on an APEX DUO instead of having to issue a drive command or drive+scan command as before. Version 2008.6 Rev 1 (2008-11-11 20:27 UTC) ------------------------------------------- * General: - Fixed a bug that prevented the successful installation of the Bruker Suite without having the database installed under Windows. * Crystal Faces: - The minimum crystal face distance that can be measured with the "T-tool" has been lowered from 0.01 mm to 0.001 mm. This is an addendum to the increase in the resolution of crystal face distances from 2 to 3 digits in release 2008.2. * Experiment: - Fixed a bug that could cause the application to crash under Windows or lock up under Linux if the user interacted with the GUI while images from an ongoing data collection were coming in and the HKL overlay was turned on. Version 2008.6 (2008-11-07 20:27 UTC) ------------------------------------- * General: - The New Sample dialog now prevents the user from entering invalid characters for the folder name. * Data Collection Strategy: - If the Refine button is clicked immediately after the resolution limit was changed, without pressing Enter, the new resolution limit is no longer ignored. Also, the "Status not idle" error message no longer appears in this case. - The exposure time controls are no longer clipped off. - A Python error could occur if the user stopped the scanning process after starting the strategy refinement. * Experiment: - Runs with scan direction "automatic" were restored as either "positive" or "negative" when an exported experiment was imported. The scan direction of a run could sometimes be inverted after it had been imported. These two issues have been resolved. - Invalid Omega runs on fixed-Chi goniometers could incorrectly be identified as valid, resulting in limit violation errors in BIS. - A Python error occurred if a run was shorter than the width of one image. - A Python error occurred on instruments with an AXIOM detector if, at the time the plug-in opened, the detector was at a distance larger than the maximum valid distance, e.g. at the dx home mark. * Generate Report: - The Acta Crystallographica C/E report template now clears the CIF items _exptl_absorpt_process_details, _exptl_absorpt_correction_T_min, and _exptl_absorpt_correction_T_max if the absorption correction type is set to "none". - Improved the handling of the publishing authors' list. The editable fields are now wider, a change in color indicates the transition between the columns, and a default text encourages the user to enter the author's name and address. * Integrate Images: - The column widths in the run list table now adjust to improve the visibility of the input and output file names. - Changed the inter-component constraint defaults so that twin domains always share the same unit cell parameters. - AXIOM images are now identified to the SAINT integration engine as coming from a PXC type detector, if SAINT v7.60A or later is used. This is the first version of SAINT that makes a distinction between MULTIWIRE and PXC detectors. * Simple Scans: - Driving the goniometer or making a scan immediately after an anode change on an APEX DUO sometimes gave an error message claiming, incorrectly, that the requested position or scan was not possible. * Unwarp and convert images: - The detector distance in the image header list is now limited to 1000 mm instead of 100 mm as before. - Added the detector distance offset, aka cm-to-grid distance, to the list of editable image header properties. Version 2008.5 (2008-09-12 19:27 UTC) ------------------------------------- * General: - Added support for the APEX2S detector. - Added support for shutterless data collection with the AXIOM detector. - The detector distance that was sent to the Bruker Instrument Service for retrieving the spatial of an AXIOM detector was specified in millimeters and not in centimeters. - In the instrument status window only the message list will now resize when the window is resized and the status list stays put. - Some parameters were not properly reverted back to their previous values when the database session was discarded. - The standard deviation shown in the image display for the rectangle tool was calculated incorrectly by a factor of N**(-1/2), where N is the number of pixels in the rectangle. * Crystal Faces: - The center of the T-tool did not move when the center of the microscope was changed (only the crystal polyhedron moved). For thin plate-like crystals this meant that if the center was outside the crystal, the crystal faces could not be assigned. * Data Collection Strategy: - Entering 0.0 for the 2Theta resolution limit or for the sin(Theta)/lambda resolution limit caused a Python error. Both parameters are now limited to a minimum value of 0.01. * Determine Unit Cell: - Fixed a rare error condition that caused a Python error if the user started the indexing process, cancelled it, and then started another indexing process shortly after. * Diffraction Space Viewer: - Samples with a low intensity range no longer cause problems with the slider or color ramp value range scaling. * Experiment: - Removed the internal time target of 24 hours from the New Strategy wizard. * Generate Report: - Added a report template for Acta Crystallographica C/E CIF files. - Added tabs to sort the lists of atoms, bond lengths, bond angles, torsion angles, hydrogen bonds, and publishing authors. If the report template makes use of the CIF publication flags, the lists of bond lengths, bond angles, torsion angles, and hydrogen bonds will show check boxes for the purpose of setting/unsetting the publication flags. - Added the torsion angles and hydrogen bond tables to the APEX2 HTML report template. - The generator voltage and current settings in the APEX2 HTML report's run list were incorrect for runs that followed after an anode change on an APEX DUO. * Integrate Images: - Hexagonal crystals are now integrated with point group -3 instead of 6/m. - The "Integration Progress" list no longer scrolls to the top between updates. * Simple Scans: - Clicking the "Current" position button now sets the display for the anode to the currently used anode if the connected instrument is an APEX DUO. - Disabled the context menu options for displaying and configuring the HKL overlay for the displayed images. - Defaulted the exposure time for 360 deg Phi scans to 60 seconds. * Transform Unit Cell: - The "pre-transform" menu was renamed to "rotate" . - "rotations" work on the final cell too (Bug fix!). - Selecting a cell automatically "Go" with it. - "Go" button was removed from the user interface. Version 2008.4 (2008-07-18 17:54 UTC) ------------------------------------- * General: - The line tool in the image displays no longer resizes the graph when the line cursor is moved between high intensity and low intensity regions of the image. * Center Crystal: - Added a new configuration variable, "wrapphi", which, if set to False, will make sure that clicking the Phi90 or Phi180 buttons will rotate the Phi axis always in the clockwise direction. The default setting of "wrapphi" is True. Note that a setting of False may not be compatible with some older Bruker instruments. * Data Collection Strategy: - The pull-down list has been replaced with three separate buttons to refine or sort the data collection strategy or to replace the run list with a hemisphere data collection strategy. - The plots and statistics are no longer updated automatically when a parameter is changed, although this is still true for parameters that modify the basis set, i.e. detector distance, resolution limit, and wavelength. To instruct COSMO to recalculate, the user is required to click a new button, called Update Plots and Statistics. - Runs were not imported from the Experiment plug-in if the run list contained non-scan operations such as stills. - The plug-in became unresponsive if an attempt was made to refine a run list that contained no runs. * Determine Unit Cell: - In previous releases it was possible to open multiple histograms from the refinement dialog. This behavior was unintentional. * Diffraction Space Viewer: - Removed the toolbar because it is not consistent with other plugins. - Fixed the list of VTK errors showing up when activating the 2D plane widget. - Fixed the 2D plane widget plane image creation. - Fixed an inaccuracy in the 2Theta clipping. * Generate Report: - New plug-in for report generation. * Integrate Images: - The crystal system constraint in SAINT is now set to "0" for triclinic crystals instead of "1" as before. The difference is that for a crystal system constraint of "0", SAINT does not perform a constrained global refinement, which for a triclinic crystal is a no-op anyway. The other positive effect is that SAINT will write the correct minimum and maximum theta angles of the reflections used for the unit cell determination to the P4P file, whereas for a crystal system constraint of "1" SAINT writes 0.0 in both cases. - If SAINT v7.48A or later is used, the timeout for SAINT waiting for new images is now the larger of the timeout determined from already existing images and the timeout defined in the default SAINT.INI file. This makes it possible to tweak the maximum timeout in case network latencies or instrument latencies would otherwise cause problems. The default timeout in the SAINT.INI file has been set to 10 minutes. * Oriented Scans: - In previous releases a Python error could occur at high Psi angles. * Precession Images: - The resolution circle was not correctly centered on off-origin precession images, e.g. 5kl, if the out-of-plane unit cell axis was not orthogonal to the plane, i.e. for triclinic, monoclinic, or hexagonal unit cells. * Unwarp and convert images: - Unwarped images could show artifacts including negative pixels along the left and top edges. Version 2008.3 (2008-05-23 15:53 UTC) ------------------------------------- * General: - P4P files with an Omega or Chi zero position of <= -10 degrees or >= 100 degrees caused a Python error on import because the numbers in the P4P file would run into each other. The error should no longer happen provided the file adheres to the correct fixed format of a P4P file. * Scale: - Numerical Absorption Correction: read the faces in with SADABS, rather than XPREP. * Calibration from the command line: - caldx could give a stack trace if it was not given an explicit list of file names. * Center Crystal: - A Python error occurred if a user position without a Chi angle was used on an instrument with a Kappa goniostat. The user position will now be ignored. * Data Collection Strategy: - Reduced the delay between updating the resolution graph and the time graph during strategy refinement. This is particularly noticeable under Windows. * Diffraction Space Viewer: - Fixed the scale of the new logarithmic dual sliders. - Moved the intensity lower limit from one to zero. - Fixed the logarithmic dual color slider to work with intensities less than one. - Fixed the intensity range sliders and matching spin boxes to work with intensities less than one. - Rearranged the GUI to be less cluttered, separate the runs data selection from the VTK 3D files, and in the process create more room for the 2D plane image. * Experiment: - The resume function was broken for non-CCD detectors. - Network problems arose on systems that had the Run command removed from the Start menu. Doing so disallows the use of UNCs with the result that BIS is unable to write images to a network location that is not mapped to a local drive letter. - When being edited, cells in the table sometimes had their background turn red as an indication for invalid input, even though the entered value was valid. * Integrate Images: - Matrix runs that were collected on an APEX Duo were not deselected by default in the "Find Runs" dialog. These runs start with "cu_matrix" or "mo_matrix". * Reciprocal Lattice Viewer: - Fixed a bug that would crash RLATT while obtaining spots from the database in certain cases where data from dual wavelengths caused a math domain error. - Changed the behavior so that when the reflections are significantly altered (such as when deleting reflections) the rotation orientation isn't reset, nor are the visible groups. * Space Groups and Statistics: - Fixed a bug that would not allow a user to change the Space Group after first changing the Bravais type. - Fixed a bug that would not allow a user to revert to the original Bravais type after first clicking on a different Bravais type. * SaintPlus: - Set the default folder for files read into Scale to the last opened folder. * SHELXTL: - Set the default folder for files read into Space Groups and Statistics and Structure Solution to the last opened folder. * Structure Refinement: - Protect the plug-in from files with invalid pseudo-ASCII characters ranging from ASCII value 128 (0x80) to 255 (0xFF) to prevent stack-tracing. * Structure Solution: - Protect the plug-in from files with invalid pseudo-ASCII characters ranging from ASCII value 128 (0x80) to 255 (0xFF) to prevent stack-tracing. * Unwarp and convert images: - A Python error occurred when Bruker images with negative pixel intensities were converted to MAR images. The conversion is still not possible but a proper error message is now displayed in this case. * View Images: - Image files in MAR IP format were not loaded correctly under Windows. Version 2008.2 (2008-03-28 20:34 UTC) ------------------------------------- * Scale: - Updated the way .png files are generated. - Updated the plug-in to accommodate SADABS version 2008/1. - Updated the version of XPREP-T in the numerical absorption correction to 2008/2. * Crystal Faces: - Lowered the minimum distance for crystal faces from 0.01 to 0.001 mm. * Determine Unit Cell: - Increased the default number of digits for the q-vector components from 2 to 5. - The user is now prevented from harvesting off of still images, a condition which previously caused a Python error. - A Python error occurred in rare cases with the least-squares indexing method (aka CELL_NOW) because the minimum estimated unit cell dimension could be zero. - Refining the goniometer zero angles also refined the 2Theta zero position. If the detector orientation was refined at the same time, this resulted in large parameter correlations. * Diffraction Space Viewer: - Fixed a problem with the lower end of the color scale. - Changed the intensity sliders to logarithmic ones like those used for frame viewing, since the intensity concept is the same. * Experiment: - The Data Collection Strategy wizard did not use the current detector distance if the connected instrument had a manually operated detector track. - The resume function did not work properly if the Bruker Instrument Service reported invalid temperatures for the low temperature device. - A Python error occurred if an experiment was imported while no connection to the instrument existed. * Integrate Images: - For the SAINTplus application, all file dialogs now open by default in the most recently visited directory. - The spot position overlay did not work for the integration of incommensurate data sets. - A Python error could occur immediately after the integration of an incommensurate data set finished. * Space Groups and Statistics: - Updated the version of XPREP-T to 2008/2. * Structure Solution: - Improved loading of files after long runs. - When the file dialog is opened without a connection, it opens by default in the most recently visited directory. Version 2008.1 (2008-02-01 15:18 UTC) ------------------------------------- * General: - A Python error occurred if a P4P/SPIN file was imported together with an image file whose type was unknown or could not be identified. - The 3D image display window, the rocking curve window, and the pixel dump window did not close when the plug-in they belonged to was closed. - The "All files" option in Windows file dialogs did not show files without file extension. * Scale: - When the Repeat Parameter Refinement button is pushed, the values of the Direction Cosine information is no longer wiped out. * Center Crystal: - It is no longer possible to send a position command while the instrument is busy. * Experiment: - On Kappa goniostats, instead of a 360 deg Phi run the software collected a still image. This has been fixed. * Integrate Images: - 360 deg Phi scans are now omitted when runs are imported from the Experiment plug-in. - Runs that were imported from the Experiment plug-in had incorrect run numbers if those runs followed a still scan. - The "spot position overlay" window did not have a spatial loaded when charting data were loaded from a .cht file. As a result, the window kept asking for a spatial every time an image was loaded, unless the user chose to ignore the missing spatial. - The SAINT output in the log window was truncated under Windows. - Closing and reopening the "profile snapshots" window caused the whole application to crash under Linux. * Simple Scans: - The default exposure time can now be indicated by making the corresponding entry in the simplescans_exposuretimes configuration parameter negative. If multiple entries are negative then the most negative wins. In the GUI the exposure times are always displayed as positives. - Exposure times entered in E notation were not always processed correctly and a Python error could occur if an invalid value such as "5e" was entered. - When run from within APEX2 or PROTEUM2, the Simple Scans plug-in now writes images to a subdirectory named "simple_scans" inside the sample directory. * Space Groups and Statistics: - The HELP information on the Lattice Type graphs has been expanded. - The text on a check box has been changed from "Overwrite Existing .hkl File" to "Create .hkl File". - Finished audit trail parameters for the Space Groups and Statistics plug-in. * Structure Solution: - When files have been previously processed in Autosolve before entering the Structure Solution plug-in, the instructions now match to method chosen. This way the user won't run XM when expecting to run XS. - Changes made to the instructions are no longer written into the .ins file until the SOLVE button is pressed. - Audit trail parameters put in the Structure Solution plug-in. Version 2.2 Rev 1 (2008-01-10 19:04 UTC) ---------------------------------------- * General: - The spatial correction tables were not downloaded from the Bruker Instrument Service if no valid flood correction was available. * Center Crystal: - The +/- drive buttons for the Automated Goniometer Head did not work and the software always complained that the instrument was not idle even though this was the case. * Data Collection Strategy: - In some cases the data collection strategy was planned for the wrong wavelength. - The dataset completeness of centered lattices was calculated incorrectly. * Determine Unit Cell: - Editing one batch of reflections erroneously deleted all other batches. - Too few spots were harvested if the detector had a baseline offset of 64. Version 2.2 (2007-12-10 20:48 UTC) ---------------------------------- * General: - Switched to the new Bruker logo. - Added support for the APEX Duo. - Support for detectors with distance dependent spatial distortions has been added. The "unwarped" configuration variable needs to be set to True. Doing so will spatially unwarp all images during data collection. - The position and size of the main window are now restored to their previous settings when the application launches. For the initial position, the software attempts to center the main window on the primary screen of a multi-head display and not center it between the screens as before. The latter approach works only on systems that correctly report the number of physical screens. - The user's database password can now be changed from a command in the Sample menu. - The time component of the time stamp for when a sample was created or when it was last modified was sometimes reset to midnight. - The user is now asked for confirmation before samples are deleted from the database. - A button for activating the optical control mode has been added to the instrument status window. - A warning is displayed if a P4P/SPIN file with a linear spatial is imported together with a distorted image or a nonlinear spatial together with an undistorted image. - In the instrument status dialog the generator current and voltage are now displayed with two decimals. - The image displays now show a warning message when a distorted image is loaded while only a linear spatial correction table is available. - Some of the image displays defaulted the wavelength to Mo K-alpha unless a unit cell had been determined. This had the effect that the resolution values displayed below the image corresponded to the wrong wavelength if an image was collected at a wavelength other than Mo K-alpha. The values were correct if the unit cell had been determined beforehand. - The detector distance displayed in the image header has been reverted back to the crystal-to-front distance and is no longer the crystal-to-phosphor distance. - The line tool in the image displays can now be constrained to the vertical or horizontal orientation by holding down the Shift key. One end of the line can now be constrained to the beam center by holding down the Control key. - The 3D image viewer now chooses a background color that contrasts with the colors in the color ramp. The coordinate axis for the pixel intensities has been added. - The title information from an imported P4P file is now stored as the compound description in the database. - A Python error occurred if a P4P file without a spatial distortion table was imported. - Exported P4P files can now be done in an 'RLATT 4' mode which creates separate P4P files for each group with group 0 reflections being in the primary P4P file, group 1 reflections being in .1P4P, group 2 reflections in .2P4P, etc. Likewise the import P4P will now look for these group designations. - A Python error occurred upon saving a sample if non-ASCII characters had been entered in the sample notes. * Center Crystal: - Buttons for the user defined goniometer positions have been added. - Alternating between opposite goniometer positions for the AGH failed on fixed Chi goniometers if the Chi angle had been recalibrated since those goniometer positions had been determined. * Crystal Faces: - The crystal dimensions that are determined during face indexing are now propagated to other plug-ins. This also means that the determined crystal dimensions will overwrite any manually entered crystal dimensions in the Describe plug-in. - The magnification of motorized zoom video microscopes was incorrectly applied. * Data Collection Strategy: - The hardware profile can now be downloaded from the instrument service. For this to work, no hardware profile must be defined in the APEX2/PROTEUM2 configuration files, the Bruker Instrument Service (BIS) must be of version 2.0.0.7 or higher, and a hardware profile must have been configured in the Bruker Configuration Program (BCP). - The unit cells were not reloaded when the user switched back to a Data Collection Strategy plug-in that was already open in the background. As a result, changes to the unit cells in other plug-ins were not picked up. The behavior was correct when the Data Collection Strategy was reopened. * Describe: - A Python error occurred if non-ASCII characters had been entered for the sample compound or the crystal shape. * Determine Unit Cell: - It is no longer possible to use special characters in the image base name that will later on cause problems when processing the images. - If the number of sweeps configured for the perpendicular matrix runs is 0 and no runs are defined with the matrixstrategy configuration variable, an attempt is made to retrieve a matrix strategy from the instrument. This requires BIS version 2.0.0.7 or higher. - If the number of sweeps configured for the perpendicular matrix runs is 1 or 2, the Omega angle will now be set to 0 or 180 deg and the Omega runs will be 90 deg apart in Phi. Only if the number of sweeps is 3 will the Omega angle be at 45 deg from the beam and Omega runs will be 120 deg apart in Phi. - Different sets of defaults for the perpendicular_matrix_runs configuration variables have been added to the default_protein() and default_noprotein() functions. - It is now possible to specify the name of an experiment file, as exported from the Experiment plug-in, in the matrixstrategy configuration variable. Runs in the experiment file supersede the perpendicular matrix runs. - An incompatibility with BIS 2.0.2.7 caused a limit violation on Kappa goniometers. - A Python error occurred if the sample directory contained an image whose file name did not contain both an image number and a scan number. - A Python error could occur if the only available image file name came from the image viewer and it contained special characters such as parentheses. - If more than one run was harvested, the second and subsequent runs were always processed starting with the first image, regardless of what the user specified as the first image number. - The background determination algorithm always used 1 for the number of correlated exposures in an image instead of the actual number, which affects the counting statistics and the I/sigma(I) calculation for the pixel intensity variances. - The harvesting algorithm could find ghost peaks around the beam stop shadow if the signal ratio between the image background and the beam stop shadow was large due to a long exposure time. - The default for the excluded resolution shells (ice-rings) has been removed. - The estimation of the diffraction limit can now be disabled by setting the estimateresolution configuration variable to False. - The least-squares indexing algorithm (aka CELL_NOW) has been added as a third unit cell determination method. Only the first domain returned by CELL_NOW is used at this point. - It is now possible to turn off the difference vector, FFT, or least-squares indexing methods by setting the new configuration variables indexvec, indexfft, or indexlsq to False. All three methods must not be turned off at the same time and doing so will result in an error message. - The control for choosing the unit cell store was sometimes sized too small to view its contents. - The resolution circle tool did not use the detector corrections that were manually entered in the index dialog. - The HKL histograms in the index dialog now display the number of indexed reflections in each tolerance bin together with the total number of reflections selected for indexing. The percentage of indexed reflections displayed in the HKL histograms now refers to the total number of reflections selected for indexing and not to the subset of centered reflections as before. - An empty unit cell was created when the user cancelled out of the dialog for choosing a unit cell if an empty unit cell had been selected in the set up dialog. - It is now possible to set the Bravais lattice type manually from the dialog that appears when the Edit button for unit cells is clicked in the main window. This feature is useful for example if a P4P file from CELL_NOW is imported and the unit cell corresponds to a centered lattice, whereas the P4P file declares it as primitive. - The Refine dialog now opens the histogram window in non-modal mode and thus allows the user to interact with the main window also, which means that for example the Refine button can be clicked while the histograms window is displayed. - The automatic mode dialog now has an abort button. - The automatic mode dialog now stores its results in the database if the process has finished but the Close button has not been clicked yet. * Determine Unit Cell using Phi/Chi - The plug-in was moved to the Evaluate category. * Experiment: - The image base name now defaults to the sample name. - It is no longer possible to use special characters in the image base name that will later on cause problems when processing the images. - Added the Data Collection Strategy wizard. - The possible Omega ranges (if any) are now displayed if the validation of a scan operation fails. - Cells in the experiment table that show a list of options when clicked on had to be clicked twice before the list was shown. The list now shows upon a single click. - Appending runs from a strategy failed to update a row if that row was currently being edited, i.e. one run would be missing from the strategy. - A Python error occurred on Kappa instruments if an experiment with a Position operation was resumed. * Integrate Images: - The diffraction limit used in the Data Collection Strategy plug-in is now propagated to the Integrate Images plug-in if the user has not defined a different diffraction limit in the Integrate Images plug-in earlier. - The default crystal system in the Refinement Options dialog could get out of sync with the Bravais lattice type in the main window. - The "Find Runs" dialog no longer selects matrix runs by default. - In some cases the presence of dark images (._dk) prevented the "Find Runs" dialog from finding diffraction images in the same directory. This is true for all places that use this dialog, e.g. the Precession Images plug-in. - The software now asks whether to overwrite existing reflection files before starting the integration. - A Python error occurred if SMART images were integrated without having available a SMART.INI or SMARTDEF.INI file to fill in the missing fiducial plate hole distance for SAINT. A built-in default for this detector parameter will now be used if no SMART.INI or SMARTDEF.INI file can be found in the directory containing the image files. - A Python error occurred with online integrations while the log window was hidden. - The chart windows are no longer cleared at the beginning of a new run if the user went back to look at some of the previous charts. - The coverage statistics charts now show the graphs for the merged data after the integration has finished or when "Integration Finished" is selected. - The reflection profiles now indicate by color the weight of the initial profile. White corresponds to a 100% contribution of the initial profile, green to a 0% contribution. This feature requires SAINT v7.34A or later. * Reciprocal Lattice Viewer: - The rotation direction has been fixed. - The ACHS flag meanings were brought in line with the rest of the software. - An incommensurate tool has been added. - 2D projections are only updated at the end of a rotation to improve the performance during a rotation, which is especially noticeable with large sets. - Pressing F1 through F3 now orient according to the axis mode instead of always orienting around the reciprocal axes. - Repeated pressing of F1 through F3 now rotate around the axis they are projected along. - CTRL and F1 through F3 now free spin 90 degrees along the viewer's X, Y, and Z axes respectively. (And adding SHIFT does a -90 spin.) * Scale: - The 'Next' button on the setup page is now disabled as soon as it is pressed. Before, two competing instances of sadabs were being created. - The data from the .xht chart files are automatically read into the GUI by the fromDatabase() method. - If the user closes the plugin while reading an .xht file, the name of the .xht chart file is saved in the database as the chart_file, and the corresponding .raw file is stored in the database. This prevents the .xht file from showing up when the user reopens the plug-in. - Error handling in the main file prevents the rare 'None' columns bug. * Simple Scans: - This plug-in is now also available in APEX2, APEX2breeze, and PROTEUM2. - The user definable goniometer positions can now be specified in a more user friendly format. Each of the four user definable goniometer positions consists of a set of six configuration variables: userpos<#> = The name of the user definable goniometer position. userpos<#>_dx = The detector distance (in millimeters). userpos<#>_2theta = The 2Theta angle (in degrees). userpos<#>_omega = The Omega angle (in degrees). userpos<#>_phi = The Phi angle (in degrees). userpos<#>_chi = The Chi angle (in degrees). The <#> in the above lines needs to be replaced by a number from 1 to 4. Only the userpos<#> variable is mandatory. The previous method of specifying user definable goniometer positions can still be used. - The detector distance range was incorrect for instruments with a maximum distance of greater than 360 mm. - The default list of exposure times can now be set with the simplescans_exposuretimes configuration variable. - A Python error occurred if the user cancelled out of a request to connect to an instrument. * Space Groups and Statistics: - Added support for space group P2(1)/n. * Structure Refinement: - Loading an INS or RES file now also has the ability to load an old revision of the file stored in the database. * Structure Solution: - Structure Refinement features incorporated into Structure Solution. Version 2.1 Rev 4 (2007-05-18 14:23 UTC) ---------------------------------------- * Determine Unit Cell: - If a P4P file is exported right after harvesting but before indexing, the resulting P4P file now contains the detector parameters from the first harvested image. Before, the detector parameters were set to their defaults in this case. - The list of tasks performed by the autopilot was occasionally too small to display all tasks and the vertical scroll bar had to be used to see the obscured tasks. * Experiment: - A Python error occurred when a "change wavelength" operation was copied to another row or changed to a different kind of operation. - The area for displaying the unit cell on the monitor page could occasionally be too small and then parts of the data were obscured. Version 2.1 Rev 3 (2007-04-04 19:03 UTC) ---------------------------------------- * General: - Exported P4P files no longer contain color attributes or a secondary color. This was necessary because the color in the P4P file ultimately ends up in the CIF file entry for the primary color and CIF checkers complained when information other than the primary color was provided. - The instrument status window no longer stays on top of the main window. - It was not possible to invoke the context menu for switching the Outlook bar between stack bar mode and tree view mode while the mouse cursor was positioned over a plug-in icon without invoking that plug-in. - In the image displays, the region of interest was clipped by one pixel horizontally and/or vertically, if the region contained the rightmost and/or bottommost pixel. * Center Crystal: - The rough automatic crystal centering positioned the detector over the back light on Kappa goniostats. This meant that the microscope images were not background illuminated and the loop position could not be reliably determined. - The rough automatic crystal centering did not take the Chi limits into account on Kappa goniostats, which could lead to limit violations. * Determine Unit Cell: - The background determination now uses a cached background only if the image files from which the background was determined have not changed. Before, if the user started over with a new crystal and collected new images, it could happen that the cached background image from the previous crystal was used. - A Python error occurred if all unit cells were deleted in the Bravais or Refine dialog. It is therefore no longer possible to delete unit cells in these dialogs. Instead unit cells must be deleted in the main dialog. * Integrate Images: - For images collected with SMART, the Be window thickness is now extracted from the SMART.INI file. Version 2.1 Rev 2 (2007-02-16 18:19 UTC) ---------------------------------------- * Determine Unit Cell: - A database error (column "none" does not exist) could occur in other plug-ins if the Bravais lattice type was never determined. * Experiment: - Due to rounding errors, an Omega run that started at an instrument limit could incorrectly be considered invalid. - A Python error occurred if the experiment exceeded the maximum number for a run, which is 99. An error message is now displayed if this happens. - A Python error occurred if the plug-in was closed while the experiment was still being transmitted to the instrument. * Oriented Scans: - The arrow buttons for the exposure time and for the scan width were dysfunctional. - The button for orientating the direct-space A axis was dysfunctional. - The unit cell list is now automatically updated if changes are made elsewhere. * Precession Images: - The unit cell list is now automatically updated if changes are made elsewhere. * Restore Archive From CD: - Null value error fixed. * Simple Scans: - A Python error occurred if the file server path was not configured. The plug-in will now write the images to the OS temporary directory in this case. Version 2.1 Rev 1 (2007-01-29 17:31 UTC) ---------------------------------------- * General: - The Cancel button on the Closing Sample dialog now works correctly when the user opens another sample (before the cancel button wrongly opened the other sample without closing the current sample and it left the current sample locked). - SMART images with 2 or 4 bytes per pixel showed negative pixel counts for pixel intensities above 32767 or 2147483647, resp. - A Python error could occur if a plug-in was unable to launch. - A Python error could occur if the log file was write protected. - Under Windows, the image displays did not save PNG files of zoomed in views correctly. * Determine Unit Cell: - In the Harvest dialog, if the user clicked the left mouse button inside the scale or trough area of the I/sigma(I) slider, the slider button would not move just a single tick but repeatedly until reaching the left or right limit. This happened only on Linux systems and not under Windows. - In the Refine dialog, parameters whose values are constrained to be the same now also have the number of significant digits displayed in the GUI constrained to be the same. * Experiment: - Due to rounding errors, an Omega run that started at an instrument limit could falsely trigger an internal sanity check and cause a Python error. - Omega runs that needed to be split into two runs before data collection were not restored when an experiment was imported from a file. - The order of operations in the experiment got scrambled when the database was vacuumed. * Integrate Images: - The application of pre-existing dynamic active masks is now officially supported. In earlier versions it was possible, quite unintentionally, to enter "$DYN" as the name of a pre-existing static active mask to enable dynamic active masks. However, this "feature" got lost at some point. - A Python error occurred if the "Refinement Options" dialog was opened when no unit cell was available in the database. - A Python error occurred if SMART images were integrated without having available a SMART.INI or SMARTDEF.INI file to fill in missing detector parameters for SAINT. Built-in defaults for the detector parameters will now be used if no SMART.INI or SMARTDEF.INI file can be found in the directory containing the image files. - The charts for the completeness/redundancy statistics, Bijvoet pair statistics, and expected/observed number of reflections statistics were missing when SAINT v7.34A or later was used. - A Python error occurred if integration with SAINT failed to the point that non-printable floating point numbers such as -1.#QNAN or 1.#INF were sent over the socket connection. - A Python error could occur in rare cases when the last plotted point of a chart was clicked during integration. - In some cases the wrong runs were appended from the "Find Runs" dialog. This is true for all places that use this dialog, e.g. the Precession Images plug-in. - A memory leak has been fixed. * Restore Archive From CD: - Bug caused from CD burner never being set up has been fixed. * Scale: - The 'Next' button on the setup page is now disabled as soon as it is pressed. Before, two competing instances of sadabs were being created. - The data from the .xht chart files are automatically read into the GUI by the fromDatabase() method. * Transform Unit Cell: - New unit cells no longer have the same colors as the unit cells they originated from. Version 2.1 (2006-09-29 19:30 UTC) ---------------------------------- * General: - P4P files can now be exported specifically for the use with CELL_NOW. If such a special P4P file is used as input for CELL_NOW and if CELL_NOW is started with the -t switch, the resulting P4P file contains information about the domain(s) each reflection belongs to. This means that when the output P4P file is imported into APEX2/PROTEUM2, the reflections are automatically sorted into reflection groups, which then allow the individual refinement of twin domains. - Remote database access is now possible. - Plug-in menus sometimes shifted positions when the user switched between plug-ins. - Added the Help menu. - Split the Instrument > Connection menu command into Instrument > Connect and Instrument Disconnect. This resolves the problems that resulted from using the connection dialog also for disconnecting the instrument. - The BIS host is now pre-configured to "localhost". - The instrument status window now displays the estimated completion time for the experiment if the connected instrument is controlled by BIS 2.0. - A tool button for stopping the instrument has been added to the tool bar. - The pixel dump table in the image displays is now read-only. - The detector distances in the image display header table now are the crystal to detector-front distances and not the crystal to phosphor distances. - A Python error occurred if the overlay of an image display predicted exactly one reflection. - In the image displays the label "RMS" in the rectangle tool editor has been changed to "Std. Dev." There had been confusion of RMS(average) over RMS(counts). - In the image displays the context menu for the color bar always showed all color ramps regardless of the product line (XRD or SCD) to which the current application belonged. - The mouse wheel has been disabled in the image displays. - Switching to logarithmic color ramps could cause a Python error with some images. - The Archive / Restore / Delete icons were removed from the tool bar. * Archive To CD: - If a blank CD is already in the drive do not ask for a blank CD. - Fixed a path bug in the Burn Device setup. * Archive To File: - Newly added archive method. * Crystal Faces: - Crystals with corners of more than 3 adjacent crystal faces were not rendered correctly and the open/closed indicator was wrong. - Only the name of the initially acquired or loaded video zip stream file was stored in the database. The names of subsequently acquired or loaded files are now stored in the database too. - Increased the number of decimal places for crystal face distances to 3. - A Python error occurred if the mouse wheel was turned while the plug-in was still loading. - A Python error could occur if the video zip stream file was corrupted. * Data Collection Strategy: - Changes made immediately before closing down the plug-in or switching to a different plug-in were lost. - The plug-in did not launch if closed and opened in quick succession. * Describe: - The sample notes have been moved to the Sample menu. This allows access to the notes from anywhere in the program without having to go to the Describe plug-in first. * Determine Unit Cell: - If the detector distance defined in the perpendicular_matrix_runs_distance configuration variable is too short or too large to be accessed by the connected instrument, the detector distance will now default to the shortest possible or largest possible distance, resp. - The default I/sigma(I) level for harvesting images and indexing spots can now be set with the new configuration variable "ioversigma". This variable has also been added to the default_protein() and default_noprotein() functions. The default for protein applications is 5.0. The default for small molecule applications is 20.0. - The effect of the Omega axis zero angle was applied incorrectly for the calculation of the reflection overlay. Calculations for the least-squares refinement were correct, however. - The Bravais button now shows a gray light only when the Bravais lattice type is truly unkown. Before, the light would be gray for Triclinic P lattices as well. - The Refine button now shows a green light if the Bravais lattice has been determined and if at least one cycle of least-squares refinement has been performed for the selected unit cell. - The colors of unit cells is now preserved when a unit cell is deleted from the beginning or the middle of the list. - The order of reflections is now preserved when the reflection list is edited. - The harvest progress dialog sometimes counted to 100%, disappeared, and then reappeared to count to 1% or 2% before finally disappearing. - A Python error occurred if the plug-in was closed while the automatic unit cell determination was still running. - The histogram dialog in the refinement page displayed Angstroms as the unit for the rotation angle instead of degrees. * Experiment: - Added support for low-T device control. Currently, this has been tested for the Oxford Cryostream and the Oxford Cobra. - It is now possible to specify the number of exposures per image. - The attenuator check box is now disabled if the connected instrument does not have an attenuator. - When resuming a data collection, the existing images are scanned only once now instead of three times as before. This greatly reduces the overhead, especially for data collections with many runs. - When the generator is at standby, the resume function now compares existing images with the user settings to which the generator will be ramped up before data collection. Before, the resume function would use the current settings, i.e. the standby settings, for comparison and collected the entire data set again. - Phi 360 scans now support frame correlation when connected to an instrument with BIS v2,0,0,6 or higher. - Limit violations on P4 goniostats were not correctly detected. - A warning is displayed when the experiment is exported on an already existing file, giving the user the chance to prevent overwriting the file. - An error occurred if the file dialog for exporting the experiment was cancelled. - Cells in the spread sheet containing spin box editors, e.g. the time column, can now be edited like the other elements, i.e. typing into a cell that does not have keyboard focus will start the edit process, clear the current value, and replace it with the entered key. * Integrate Images: - It is now possible to integrate datasets with runs that were collected at different detector distances. SAINT v7.29A or later is required. - Changes to the run list table were not accepted for integration if the edit process had not been completed (by hitting Enter or changing the keyboard focus). Starting the integration is now interpreted as the user's intent to accept those changes. - The charts for the periodically refined parameters showed two additional data points for the last image of the last run. They were the constrained and unconstrained globally refined values for these parameters. The additional data points are no longer plotted. - The charts for the periodically refined unit cell parameters now display the parameter ESDs as error bars instead of as separate curves. - Some charts (e.g. those plotting the periodically refined unit cell parameters) sometimes displayed the same figures more than once along the Y or Z axis. - Improved the performance of the charting process. - The maximum number of reflections for the global parameter refinement has been increased from 9999 to 99999. - The number of twin components has been increased from 4 to 8. The additional components are accessible only with SAINT v7.29A and later. - It is now possible to prevent SAINT from waiting for the next image during an online integration process. - When the number of images in a run was edited, instead of beginning with the current value, the number was always reset to 1. - A .cht file is now automatically written when the plug-in is closed. Before, a .cht file was written automatically only if the "Close" button in the integration tab was clicked. - A Python error occurred when a run with whitespace in the image file names was integrated. - A Python error occurred if an invalid path was entered in the "Find Runs" dialog. This is true for all places that use this dialog, e.g. the Precession Images plug-in. - The "Find Runs" dialog now has two additional buttons for selecting and deselecting all runs. This is true for all places that use this dialog, e.g. the Precession Images plug-in. - When a second integration process was started in addition to one that was already in progress, the charts for the first integration process were plotted in both. - An OpenGL error occurred in SAINTchart if the Auto-Structure plug-in was running at the same time. * Oriented Scans: - An oriented scan is now performed even if an identical image with the same file name already exists. * Refine Structure: - Spawning XP did not work under Linux. * Restore Archive From CD: - When archive information is obtained from a CD, now check to see if that archive name is allowed instead of assuming that it needs to change. - When the window opens, check to see if an archive CD is inserted and automatically load that archive information it one is. - When a restore is finished, update the list of archives to include the newly restored archive's name. - Sort the list of existing samples by name. - If you change the CD burner Drive Specifier the archive information will be refreshed from this new location. - When starting to restore an archive, do not ask for the first CD if it is already in the drive. - Fixed a path bug in the Burn Device setup. - Now disables input fields when the CD inserted isn't a valid archive. - Enable/disable the group name combo box along with the other input fields. * Restore Archive From File: - Newly added archive method. * Simple Scans: - Rearranged GUI layout. * View Molecule: - Fixed crashing when saving an image of the scene. Version 2.0 Rev 2 (2005-12-06 19:22 UTC) ---------------------------------------- * Crystal Faces: - The plug-in was not displayed when a video zip stream file had to be collected on startup. * Determine Unit Cell: - Orthorhombic C-centered unit cells could have the wrong axis setting. Version 2.0 Rev 1 (2005-11-16 21:05 UTC) ---------------------------------------- * General: - The image display caused an error when the user's list of default header items could not be read from the hard disk due to file access violations. * Calibration: - Disabled plug-in. * Experiment: - Spin boxes in the table were deleted if edited before double clicking them. * Integrate Images: - A Python error occurred if the user switched to another plug-in and back again while a cell in the table was being edited. Version 2.0 (2005-11-04 20:46 UTC) ---------------------------------- * General: - The logging module caused a stack trace if the software was started in a directory without write permission. Version 1.0 Rev 37 (2005-10-12 20:28 UTC) ----------------------------------------- * Center Crystal: - The rough automatic crystal centering was broken. * Experiment: - Fixed a problem with the validation of Omega runs. Version 1.0 Rev 36 (2005-08-01 18:55 UTC) ----------------------------------------- * General: - In the image displays the background contrast level of extremely weak images (less than 5 counts per pixel) could not be adjusted to a point where the background was visible. * Center Crystal: - Fixed a problem with the new semi-automatic crystal centering tool that prevented the video microscope images from being displayed under MS Windows. Version 1.0 Rev 35 (2005-07-22 21:17 UTC) ----------------------------------------- * General: - Corrected a version mismatch in one of the user interface files. Version 1.0 Rev 34 (2005-07-22 20:25 UTC) ----------------------------------------- * General: - In the image displays the 3D image view caused an error if the selected region was only one pixel wide and/or high. - In the image displays the resolution circle tool sometimes drew stray lines on the screen. - In the image displays the rocking curve dialog expanded the angle range to 360 degrees if the analyzed range included negative and positive angles. * Center Crystal: - The automatic loop centering can now be performed at three different levels of accuracy (rough = two positions, good = 15 positions, best = 30 positions). - A tool for semi-automatic crystal centering has been added. The user is presented with two images of the crystal and upon clicking on the crystal in each image, the Automated Goniometer Head moves the crystal to the instrument center. - Message boxes now appear on top of the buttons that triggered the messages. This reduces the chance of having a message box hidden behind the Video program, eluding the user's attention. * Determine Unit Cell: - Many of the noise pixels that were harvested before at very low I/sigma(I) levels are now filtered out. Version 1.0 Rev 33 (2005-05-25 18:59 UTC) ----------------------------------------- * General: - Corrected the path the Windows installers of Proteum2Server and Proteum2Screening set in the Start menu. - Database samples to which the user has no read access no longer cause a stack trace when being accessed by the file open dialog. * Center Crystal: - Reduced the number of detector distance changes when switching between goniometer positions. - The detector distance is no longer changed during the automatic crystal centering if the current distance is already larger than the minimum distance needed. * Experiment: - The runs imported from the strategy planner now have sweeps of a multiple of the image width used in the data collection plugin. Before, the values could be slightly greater, although this had no impact on the data collection itself. - 360 degree Phi scans were not dark current corrected and flood field corrected. * Determine Unit Cell: - Improved image harvesting algorithm. The software now finds more spots at the same I/sigma(I) level and also finds spots that were impossible to harvest before. As a downside the algorithm at very low I/sigma(I) limits now may also harvest noise pixels. - Improved the least-squares refinement of unit cell parameters. The previous implementation could become numerically unstable on computers running a Windows operating system. * Integrate Images: - The initial box size in X and Y was underestimated for images with 1024 or more pixels. Version 1.0 Rev 32 (2005-02-25 19:52 UTC) ----------------------------------------- * General: - Closing Apex2 or Proteum2 with the [X] button in the window title bar now allows to cancel the program shutdown. Version 1.0 Rev 31 (2005-02-17 17:49 UTC) ----------------------------------------- * Center Crystal: - The Video program is now sent to the foreground whenever the plugin is launched, activated, or any of the position buttons is clicked. Version 1.0 Rev 30 (2005-02-17 15:20 UTC) ----------------------------------------- * Center Crystal: - The mount position for the Automated Goniometer Head (AGH) is now at a Chi angle of 54.74 degrees to prevent the AGH from icing up. - The detector distance for the mount position during manual centering is now determined dynamically and not, as before, set to the maximum distance. Version 1.0 Rev 29 (2005-02-16 13:43 UTC) ----------------------------------------- * Center Crystal: - Added workaround for a bug in BIS 1.2.1.7. Version 1.0 Rev 28 (2005-02-15 14:12 UTC) ----------------------------------------- * General: - Phi angles are now rounded to the [0..360[ range before being sent to the Bruker Instrument Service. In the past this has caused some Phoenix and GGCS controllers to lock up. - Resolved an incompatibility with BIS, where for newer versions of BIS (reportedly 1.2.1.6) the wrong minimum detector distance was determined for instruments without a motorized dx track. * Center Crystal: - Extended the position database to the goniometer positions needed for manual centering with the AGH. * Describe: - Fixed the tab order of widgets. * Determine Unit Cell: - Changing one of the Yes/No flags in the reflection list caused a Python error. * Experiment: - On Windows machines the image directory path was corrupted when no local network was available. * Integrate Images: - The validity of the resolution limit was not enforced and could result in a Python error. * Reciprocal Lattice Viewer: - Fixed bug where groups marked as non-visible always had their checkboxes checked when RLATT began, regardless of visibility. * SaintChart: - SaintChart did not start if the log file in the target directory could not be created or written to. - If a run was integrated twice (e. g. because of missing images) the combined chart data was displayed for the first run and the charts for the second run remained empty. - When opening an existing chart file (.cht) all charts began at image number 0 if the images themself were not available. Version 1.0 Rev 27 (2004-10-12 14:23 UTC) ----------------------------------------- * Data Collection Strategy: - Cancelling a connection request when changing to "Data Collection Strategy" from a different plugin caused a Python error. The user is now informed about the problem and the plugin shut down. * Determine Unit Cell: - The entry for the first image file name now reacts to file system changes in realtime. Version 1.0 Rev 26 (2004-10-04 17:11 UTC) ----------------------------------------- * General: - Instrument axes for which the Bruker Instrument Service wrongly reports a resolution of 0.0 now are defaulted to a reasonable value. - The software now detects the absence of a local network under Windows and on systems that run the Bruker Instrument Service on the same computer as the client software, local paths will be sent to BIS if no network exists. * Center Crystal: - The Chi angle for manual AGH control has been limited to 54.74 degrees to prevent icing problems which otherwise occurred at the previous maximum Chi angle of 90.00 degrees. * Data Collection Strategy: - Leaving an input value in an illegal state (indicated by red background) when moving to a different input value resulted in a Python error. The last valid value is now automatically restored in such cases. * Integrate Images: - Incomplete rows in the run list table caused Python errors. Version 1.0 Rev 25 (2004-09-24 12:12 UTC) ----------------------------------------- * General: - This "changes" document is now a part of the Windows and Linux distributions of SEATTLE. * Center Crystal: - The "+" and "-" buttons could get stuck in the pressed down state when the "instrument is not idle" error message was displayed. * Experiment: - The default parameters for the perpendicular matrix runs had been changed inadvertently. They are now reverted back to their original values. - The extra overhead of repeatedly retrieving the wavelength from instruments with tunable wavelengths has been greatly reduced. * Integrate Images: - The standalone version (SaintPlus) is working again after a bug in in the database module had disabled it in the previous version. * SaintChart: - The progress statistics was not calculated correctly for the integration of twins. * Simple Scans: - The scan range now always equals the image width after one of the "Narrow", "Wide", "Still", or "Phi 360" buttons has been clicked. Version 1.0 Rev 24 (2004-09-07 17:41 GMT) ----------------------------------------- * Center Crystal: - Fixed a bug in the position database. * Experiment: - Interrupting the connection to BIS caused a Python error on instruments with tunable wavelength when the experiment was executed or resumed. Version 1.0 Rev 23 (2004-09-03 13:01 GMT) ----------------------------------------- * General: - The browse button of an image view opened the file dialog in the wrong directory. - The image display did not show the last row/column of an image. - The image header table in the image display now shows the beam center in warped pixels instead of in millimeters. - Fixed a bug in the 3D view that opens from the image display. - The CCD temperature display in the status window is now updated on a regular basis even if no data is being collected. - Implemented a cross-client procedure for instrument aborts. All clients will now abort their instrument activities when a hard abort or soft abort is issued from any client. * Center Crystal: - Switching from an Eulerian-type instrument to a Kappa-type instrument during one session of the software resulted in the wrong base angles being used for the various goniometer positions. - The time delay in driving from one goniometer position to another has been shortened considerably. - A new button ("Mount") has been added to the page for motorized crystal centering. This button homes the automated goniometer head (AGH), drives the AGH to the instrument center, and drives the goniometer to the mounting position. - A new button ("Alternate") has been added to the page for motorized crystal centering. This button alternates between the two corresponding goniometer positions for the currently selected direction. This is the same as repeatedly clicking the X, Y, or Z radio button. * Data Collection Strategy: - The wrong wavelength was used on non-Mo systems when a strategy was made without having determined the unit cell before. - A warning message is now displayed if COSMO cannot be contacted due to a blocked TCP/IP socket. This warning indicates that a firewall may be preventing the socket connection from being established. - The speed of the hemisphere strategy determination has been greatly improved. * Determine Unit Cell: - The vertical beam center position as imported from the image header was always off by the size of one pixel. * Experiment: - The support for instruments with tunable wavelengths added an overhead to systems with fixed wavelengths as well. This has been changed at the downside of having to reconnect to the instrument if BIS is reconfigured on the fly from non-tunable to tunable wavelength. - Illegal runs defined in the matrixstrategy configuration parameter caused a Python error. - Split the "Execute / Resume" button into two separate buttons, "Execute" and "Resume". - Display a message if an experiment is being resumed when all scan operations are already performed. * Integrate Images: - The "full scale" value for CCD detectors is now retrieved from the image header by SAINT itself. This allows changing full scale values between runs or within a run to be handled correctly. This feature is available with SAINT V7.10 and later. Older versions of SAINT will be provided with a full scale value as before. - The "base line offset" for CCD detectors was not correctly forwarded to SAINT. The value is now retrieved from the image header by SAINT itself, if SAINT V7.10 or later is available. Older versions of SAINT will be provided with the corrected value. - The "Import Runs from Experiment" feature skipped runs that need to be inverted prior to data collection. - The "Import Runs from Experiment" did not ignore "Still" operations and "Position" operations from the "Experiment" plugin. This resulted in Python error messages being displayed. - The mouse cursor now changes to an hourglass while the "Import Runs from Experiment" feature is busy. - The browse button in the "Find Runs" dialog did not open in the specified directory. * Reciprocal Lattice Viewer: - Fixed a bug when adding a spot to a group that spot now is hidden if that group is not visible. - Added the missing explanation for the ALT key functionality to the key commands What's This help. Version 1.0 Rev 22 (2004-05-24 17:07 GMT) [released: Linux, Win32] ----------------------------------------- * General: - Using the directory browser in "File > New" did not go to the correct folder. * Data Collection Strategy: - On startup the data collection strategy now contains only the active runs from the Experiment plugin and ignores all other operations. Version 1.0 Rev 21 (2004-05-22 17:07 GMT) ----------------------------------------- * General: - The name of a sample can now only contain the characters A-Z, a-z, 0-9, and _. - The header table at the bottom of an image view now includes the number of exposures for the currently displayed image. * Center Crystal: - The "Center" position for fixed-Chi diffractometers (D8) is now under the microscope camera. * Experiment: - Added "Wavelength" operation to support instruments with tunable wavelengths (primarily synchrontrons). * Integrate Images: - The "Import Runs from Experiment" feature sometimes skipped images at the beginning of the experiment. * Reciprocal Lattice Viewer: - Fixed a bug that prevented the "Export Visible Spots to P4P" button in the Edit window from working. - Fixed the vertical line bug in the "Lattice Overlay" selection tool where the angle used for selection was wrong whenever there was no change across Y for the two points used by the tool. - Fixed a bug where the spot size wasn't being used for the "Lattice Overlay" selection tool. Spot size now matters. Version 1.0 Rev 20 (2004-04-29 20:09 GMT) ----------------------------------------- * General: - Archived log files would grow exponentially under MS Windows if the archiving took place more than once a day. This bug has been fixed. Version 1.0 Rev 19 (2004-04-27 21:25 GMT) ----------------------------------------- * General: - Under MS Windows the DOS command prompts for the Apex2, Proteum2, SaintChart, and Screening packages are now hidden. - Archived log files were corrupted under MS Windows. This bug has been fixed. * Experiment: - Fixed a bug that would sometimes send invalid Omega runs to the Bruker Instrument Service. This problem occurred on X8 based instruments only. * SaintChart: - A proper error message is now displayed if the user tries to open a .cht file from the Scale plugin. The extension for chart files written by the Scale plugin has been changed since, so this modification is for compatibility with existing files only. Version 1.0 Rev 18 (2004-03-12 16:12 GMT) ----------------------------------------- * General: - Fixed problem with the conversion of Chi to Kappa and vice versa. - The vertical pixel coordinates shown in the image display are now according to the original Bruker convention, i. e. the first row of pixels is at the bottom of the image. * Experiment: - The position goniometer operation no longer displays a warning message about overwriting an image file. - The detector parameters (pitch, roll, yaw, beam center, distance error) are now taken from the least-squares refinement instead of the image header. - Added a new configuration parameter (perpendicular_matrix_runs_frametime). It defines the per-image exposure time for the matrix runs. The default value is None, which causes the runs to use the global exposure time as defined in the Experiment plugin. * Integrate Images: - If started as a standalone program (SaintPlus) the default location for SAINT output files is now relative to the current working directory. * View Images: - The detector parameters (pitch, roll, yaw, beam center, distance error) are now taken from the least-squares refinement instead of the image header. Version 1.0 Rev 17 (2004-03-01 20:42 GMT) ----------------------------------------- * Integrate Images: - Fixed Python-2.3 related bug in the "Integration Options" dialog. Version 1.0 Rev 16 (2004-02-27 22:33 GMT) ----------------------------------------- * Generate Report: - The dialog now opens with the name of a .cif file if only one such file exists in the working directory. * SaintChart: - Added progress statistics window. * Simple Scans: - The exposure time for the 360 deg Phi scan has been limited to a minimum of 15 seconds. Version 1.0 Rev 15 (2004-02-25 14:21 GMT) ----------------------------------------- * Center Crystal: - Renamed plugin from "Align Crystal". - The detector distance for manual centering is now determined dynamically and not, as before, set to the maximum distance. This obviates the long waiting times on systems with a long and/or slow detector track. - Added controls that allow manual access to the Automated Goniometer Head (AGH) and the automatic loop centering. - Added online documentation for all controls. * Experiment: - Invalid user input (e. g. an empty field instead of a number) is now handled without causing a Python error. - A successful validation is now announced with a message display instead of the lack of an error message. Version 1.0 Rev 14 (2004-02-12 21:03 GMT) ----------------------------------------- * Integrate Images: - The "Find Runs" dialog now opens with useful defaults. Version 1.0 Rev 13 (2004-02-06 21:21 GMT) ----------------------------------------- * General: - The state of tool bar icons in the main window were sometimes out of sync with their corresponding menu commands. This has been fixed. - The "File > Export > P4P file" and "File > Import > Spatial" dialogs now have better defaults for the file names and directories. * Experiment: - The definition of the matrix data collection strategy has been simplified. Four new configuration parameters have been added: perpendicular_matrix_runs_2theta, perpendicular_matrix_runs_distance, perpendicular_matrix_runs_sweep, perpendicular_matrix_runs_nr_sweeps. The original matrixstrategy configuration parameter is still available although its default has been set to None. If matrixstrategy is set as before, it will supersede the new perpendicular_matrix_runs_* parameters. Thus it is important to remove any definitions of matrixstrategy from local configuration files for the perpendicular matrix runs strategy to take effect. - Operations are no longer deactivated after they have been performed. - The automatic subdivision of runs on Kappa goniostats has been improved, so that routes with only a few images/degrees in one run do not occur anymore. For this purpose two new configuration parameters (subdividerouteminimages and subdividerouteminsweep) have been added. These define the minimum number of images and the minimum sweep in every section of a subdivided route. * Integrate Images: - Added "Import Runs from Experiment" button. Clicking this button imports the runs defined in the Experiment plugin into the run list table for integration. * SaintChart: - The resolution circle tool and the Miller indices in the reflection overlay window are now displayed properly. - Added documentation for charts and graphs. Version 1.0 Rev 12 (2004-01-28 16:41 GMT) ----------------------------------------- * General: - The "File > New" command did not go to the correct user folder. Version 1.0 Rev 11 (2004-01-28 15:16 GMT) ----------------------------------------- * General: - The "File > Login" command is now disabled when the user is already logged in. - The "File > Open" dialog now opens much more quickly when a large number of samples is displayed. - The "File > Export > P4P file" dialog now appends the .P4P extension to the chosen file name if it has no extension. - Log files are now archived when they have reached a certain size. - Moving one of the intensity sliders in an image display beyond the other slider no longer causes an error. - Under MS Windows the database installer now repeats the question for confirmation until either "Yes" or "No" has been entered, thus giving the user a second chance in case the answer was not typed in correctly. * Determine Unit Cell: - The down-scaling of diffraction images prior to harvesting can now be turned off by setting the 'scalebeforeharvest' configuration parameter to 0. This can be necessary for datasets with very small spot sizes such as from a small crystal on a synchrotron beamline. - The H, K, and L columns in the reflection list dialog are now sorted correctly. * Experiment: - Validating or executing the list of operations when no hardware connection exists no longer causes an error. * Integrate Images: - The initial values for the integration box size are now determined from the diffraction images that were harvested during the unit cell determination. * SaintChart: - The image numbers in the graphs always started at 0. This bug has been fixed. - The diffraction image displayed and the corresponding HKL overlay were off by one image. This bug has been fixed. Version 1.0 Rev 10 (2003-12-12 19:44 GMT) ----------------------------------------- * Experiment: - HKL overlay now works properly. - Rows pasted into the run list table sometimes ended up at the bottom. This bug has been fixed. - 2Theta angles are now mapped to the ]-180..+180] degree range. * Instrument Status: - The default temperature range for CCD chips has been expanded to [-65..-35] degrees Celsius. * Xylid Test Script: - The weighting scheme for the initial refinement run is now 0. - Relevant data for the final acceptance test are now printed to the screen and written to the harddisk. Version 1.0 Rev 9 (2003-10-27 22:22 GMT) ---------------------------------------- * General: - In the image displays the resolution circle tool now correctly follows the contours. The resolution label now has a black background for better readability on bright images. - Refusal of MS Windows to retrieve the local path of shared folders no longer prevents the software from starting. A warning message is printed in this case now. The only alternative for the user is to manually enter the local shares in the configuration file. - The definition of the horizontal microscope angle has been inverted to be compatible with the SMART and PROTEUM software. This means that on all X4Apex and X4Proteum systems the horizontal microscope angle in the BrukerInstrument.ini file needs to be inverted when upgrading from releases that predate version 1.0 rev 9. X8Apex and X8Proteum systems are not affected. * Experiment: - A message box is now displayed if the user tries to execute/resume a data collection that will overwrite some image(s). The user gets the choice to either proceed anyway or cancel the data collection. - Operations are now activated automatically when the user changes the operation type. - The Generator operation now defaults to the current and voltage settings defined by the user in BIS/BCP. * Integrate Images: - The "work" directory for output files from the integration is now created in the sample folder and not, as before, as a subdirectory of the location of the images. * Simple Scans: - Images are now always collected regardless of whether or not identical images already exist in the destination folder. Version 1.0 Rev 8 (2003-10-03 21:35 GMT) [released: Win32] ---------------------------------------- * Determine Unit Cell: - Added support for circular detectors. Inactive regions of an image are now ignored during harvesting and when the HKL overlay is displayed. * Reciprocal Lattice Viewer: - Moved the "Select Visible Groups" tool from the Visualization window to the Edit window. - Added a "Delete Non-Visible" button for removing unwanted spots from the collected data. - Added a "Select Current Group" button for selecting all spots belonging to the Current Group specified in the Grouping Tools section of the Edit window. - Minor cleaning up of the user interface in other areas. * Structure Refinement: - Added the selection of a .RES or .INS file for XShell to use. Version 1.0 Rev 7 (2003-09-29 20:00 GMT) ---------------------------------------- * Data Collection Strategy: - Fixed a bug that sometimes failed to interrupt the strategy refinement when the Stop button was clicked. Version 1.0 Rev 6 (2003-09-29 18:38 GMT) ---------------------------------------- * Data Collection Strategy: - Fixed problem that ignored a changed resolution limit in either d, 2Theta, or sin(Theta)/Lambda if the cursor was immediately afterwards set to one of the other two fields. - A warning message is displayed if the user tries to refine a strategy after the resolution limit has been changed. The user is given the choice to generate a new run list for the changed resolution limit, keep the current run list, or cancel the refinement operation altogether. - The hemisphere command is now disabled if the software is connected to a Kappa goniometer. - The initial detector distance that is set when the plugin is launched for the first time on a particular sample is now taken from the runs previously defined in the Experiment plugin. If no such runs exist then a suitable detector distance is determined from the harvested reflections. - Fixed a bug that under certain circumstances could cause the plugin to freeze. * View Images: - New plugin that allows the user to display and inspect diffraction images. * Integrate Images: - The standalone version of SaintChart now accepts a chart file as an optional command line argument. It is no longer necessary/possible to specify the -c qualifier to do so. If a chart file is specified, its contents will be displayed in SaintChart, thus allowing the user to inspect earlier integrations. - The "saintchart" command has been added to conveniently launch the standalone version of SaintChart from the command line. Under MS Windows a new icon has been added to the Start menu as well. Version 1.0 Rev 5 (2003-08-21 13:27 GMT) ---------------------------------------- * General: - Fixed problem with network shares under MS Windows. The net.exe command no longer needs to be in the path. - In the image displays the X axis of the line cursor tool graph did not have the correct scale. * Align Crystal: - A check is now performed to see whether driving to the alternate Kappa position gives the user easier access to the goniometer head screws. * Data Collection Strategy: - Fixed a bug that prevented the context menu in the "Detailed Strategy" dialog from being displayed. * Determine Unit Cell: - The harvesting algorithm has been improved to find more spots on an image (especially faint ones). - The harvesting algorithm no longer filters out split reflections. This had caused problems with indexing from diffraction images that were collected at a too short detector distance. - The harvesting algorithm now performs the spot bifurcation test in both directions, to the next and the previous image in the run. * Reciprocal Lattice Viewer: - Expanded "What's This?" help with tables of keyboard commands. - Fixed bug that occured when deleting reflections. - Greatly expanded keyboard functionality. Version 1.0 Rev 4 (2003-07-25 20:57 GMT) ---------------------------------------- * Determine Unit Cell: - The I/sigma(I) slider in the Harvest dialog now has a logarithmic scale. * Reciprocal Lattice Viewer: - Added "What's This?" help. Version 1.0 Rev 3 (2003-07-18 13:37 GMT) ---------------------------------------- * General: - The session of an opened sample is now properly closed if another sample is opened or a new sample is created. * Data Collection Strategy: - Added an error message that is displayed when the configured hardware profile file does not exist. * Determine Unit Cell: - Removed the Clear button from the reflection list dialog. - Columns in the reflection list dialog that contain numbers are now sorted numerically instead of alphabetically. Version 1.0 Rev 2 (2003-06-27 21:22 GMT) ---------------------------------------- * Determine Unit Cell: - Fixed a problem with the mosaicity determination when no reflections had been harvested. Version 1.0 Rev 1 (2003-06-20 18:55 GMT) ---------------------------------------- * Align Crystal: - The 2Theta offset during crystal centering is now changed only if the connected instrument possesses a motorized DX track, which allows the detector to be moved out of the way. * Determine Unit Cell: - Fixed problem with the displayed beam center position. - The number of indexed reflections is not calculated anymore when the Index dialog initially pops up. * Integrate Images: - Removed carriage return characters at the end of the SAINT text output. * Reciprocal Lattice Viewer: - Fixed problems with z-ordering of 3D objects. Version 1.0 (2003-06-12 14:57 GMT) ---------------------------------- * Initial release.