#!/bin/sh # Collect -D & -m options as java arguments command=java while [ `echo $1 | egrep '^-D|^-m' | wc -l` != 0 ]; do command="$command $1" shift done # Determine installation location if [ "$JMOL_HOME" = "" ]; then binDir=${0%/*} if [ "$binDir" = "$0" ]; then # Ran from local directory binDir=$PWD fi # Resolve symlinks. program="$0" while [ -L "$program" ]; do ls=`/bin/ls -ld "$program"` link=`/usr/bin/expr "$ls" : '.*-> \(.*\)$'` if /usr/bin/expr "$link" : '.*/.*' > /dev/null; then program="$link" else program="`/usr/bin/dirname $program`/$link" fi done binDir=`dirname $program` fi JMOL_HOME=${JMOL_HOME:-$binDir} libDir=${JMOL_HOME}/jars if [ ! -e ${JMOL_HOME}/Jmol.jar ]; then echo "Jmol could not find its installed files." exit fi $command -Djmol.home="$JMOL_HOME" -jar ${JMOL_HOME}/Jmol.jar "$@" e'4)Ys7eDOg0(%Sn r<3ƺԄ#ntktH'IC$e\W_`)Eѓ3Lt4iu.Z#ckGX<XRY94K(qoF6=NnX#ˈh'♝Q|~Z0ͫGG.ee))%9 H6N3p$ݬM!@YM:<Ε}N<[Ocz̅D"5өQ:o#:VDbR:ɰ5tsUl:z67ex"O'!e&髞t}VՑGI:piyR0;oDi-@y=VW98r  =R"D\]Dn36gZ<`lZ jm{zi4qຢ3H 0 ^RĄO[؝o)|Zj''q igṚ(^ٕʅ/+JS?ׯMJ׽PT is@"OPKN4B =PK+:0org/jmol/adapter/readers/more/MoldenReader.classW `S>?ɽIo$ !Ki6Ev8nb[)Nqps=N{m)ln9pn>t9ޤ- i?ss9nۨy >'A;C|nhrMF p^>N{|RO iGg,{ ϑ_ppF _0F 9jƹP ю%$j&<(Mh1?F˿,W< U7| N)O MC%;<|?hwq=}<# c~?gtWAKMiPSԺM>Y)k뗿c݅OPL̥-RF)I֦]ݙE^Ő4^oLzpiES{HVU2j.e-1`ZKR Q[%t Y)ѝ l#ʩ&s>zA!(Y pS4ڹyU-%%)+nz@;!M`E~Uz%]$d5%ڰ6ͬEd[RwD;ۋl="6)&̽Cly#E\ q3汋яX*Jdl.mh@1s+dPu]XsRN!ŬǸ %i@38RK3/.jr]Y;AtRff;Dn4ږT/ E'@')i̼ʚn.izKyt-w*F)2ꪌyMcAL^Ih)Dl4S0hRD-zW3WZpP}i`@NcM- n XSbֈjBIxc4 خ^) \½CJ!fƹ.d94 )܌o-QXJ2gšUB%6tVfa"&2XBy? 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# Viewer accesses ModelSet methods directly # ModelManager streamlined substantially # # This basically removes two full layers of abstraction. # All the atoms, bonds, and models are now in ModelSet. # # code(II): ModelSet extends ModelCollection extends BondCollection extends AtomCollection # # bug fix: dipoles moved back into shape from shapespecial # bug fix: semi missing in show orientation message, second part (zyz text) # bug fix: select 0 selects all instead of PDB group 0 # bug fix: write t.xxx # ----------------------------------------------------------------------------- #version=11.3.31 # bug fix: calculate aromatic for N and O refined # new feature: valence -- sum of bond orders # print {atomno=3}.valence # {atomno=1}.valence = 3 # select (carbon and valence != 4) # new feature: settable atom properties (preliminary): # .x, .y. .z, .xyz, # .fx, .fy, .fz, .fxyz, # .vx, .vy, .vz, .vxyz, # .formalcharge, .occupancy, .partialcharge # .temperature, .valence # for example: # a = {atomno=30} # a.xyz = {1.0, 2.0, 2.3} # a.temperature = 3.0 # a.formalcharge = 2 # new feature: set atom properties using {xxxx}.x = # # {atomno=3}.x = 3 # {(*)[2]}.xyz = {1 2 3} # for(var i = 1; i < 3; i = i + 1); {(*)[i]}.x = 5;end for; # {atomno=3}.property_whatever = 2.0 # new feature: set atom properties using an array instead of a DATA statement: # {*}.property_mydata = array(1.0,5.5,4.4,3.3); # {*}.property_mydata = "3 4 5 6 7 8"; # {atomno < 4}.xyz = array({3 4 5},{4 5 6},{5 6 7}) # code optimization for within() and setAtomBits() # more export generator classes # bug fix: unitcell missing some lines when axes turned off # ----------------------------------------------------------------------------- #version=11.3.30 # new feature: adds H/Br/Cl/I/C logic to aromatic bond assignments # new feature: adds Oxygen/Sulfur logic to aromatic bond assignments # new feature: adds Nitrogen logic to aromatic bond assignments # bug fix: menu for UNITCELL # new feature: PovrayExporter (pim schravendijk ) # ----------------------------------------------------------------------------- #version=11.3.29 # new feature: aromaticSingle and aromaticDouble bond order options # new feature: "smartaromatic" bonds # turned off with "smartAromatic = false" # new feature: calculate aromatic # calculates reasonable aromatic double/single alternation. # new feature: reset aromatic # sets all aromaticDouble and aromaticSingle back to aromatic # new feature: select ISAROMATIC # selects aromatic atoms # new feature: MOL reader recognizes bond types 4,5,6,7 # new feature: isosurface/mo "squared" # new feature: fully generalized bond order "partial n.m" # n = number of lines, up to 5 # m = binary mask for dottedness, up to 31 (0x1F) # 00001 first line of bond dotted # 00010 second line of bond dotted # 00011 first and second line of bond dotted, etc. # new feature: connect may use numeric bond orders, including "partial n.m" # new feature: preliminary work on functionalized state # new feature: global/local functions (to applet, for instance # in general, functions are global -- common to all applets. # first-character "_" indicates this function is a LOCAL function, private to this applet. # ----------------------------------------------------------------------------- #version=11.3.28 # critical bug fix for color command not coloring objects properly # new feature: bondOrders 2.5 and -2.5 PartialTriple and partialTriple2 # ----------------------------------------------------------------------------- #version=11.3.27 # critical bug fix for functions not returning values # bug fix for atomarray[i] not selecting properly # bug fix for write not working with VAR # bug fix for application not accepting pastes into the # console consisting of multiple lines # bug fix for bondOrder command not properly treating 4.0 or 0.5 # bug fix for decimals not represented properly in error messages # ----------------------------------------------------------------------------- #version=11.3.26 # new feature: _1 parameter for "first atom" in second expression of connect: # connect 3.0 (_H and connected(_N) (_O and not within(chain,_1)) hbond # new feature: better reporting of PMESH file format errors # code cleanup: pmesh moved to shapespecial; privatized # bug fix within(chain,xxx) not working # bug fix for() as first command in script or line # bug fix we were not exporting error free xhtml 1.1. # bug fix for WebPageMaker not writing files # bug fix for PAUSE causes app to hang -- this is a reversion of use of SwingUtilities.invokeLater(), # which actually will not work in ScriptWindow. We need the direct execution in # order to avoid the event queue from stopping itself. # ----------------------------------------------------------------------------- #version=11.3.25 # bug fix compiler not recognizing "axes =" or "measures = " # bug fix for WebPageMaker creating uncompressed PNG # bug fix for WebPageMaker not stripping \ in load file names # ----------------------------------------------------------------------------- #version=11.3.24 # critical bug fix for 11.3.23 compiler not recognizing line endings # bug fix for show state for draw in multi-model environment # bug fix? for background model not available for multiple frame range (e.g. frame 2.0) or after invalid frame number # # new feature: within(distance,isWithinAllModels,atomExpression) # # allows finding atoms within a specified distance of other atoms in OTHER models: # # select within(5.0,true,model=2.1) # TRUE indicates we should check all models # select within(5.0,false,model=2.1) # FALSE -- only model 2.1 # select within(5.0,model=2.1) # default is FALSE # ----------------------------------------------------------------------------- #version=11.3.23 # VERSION full script flow control support: # if / else if / else / end if # for / end for # while / end while # # var i = 4 # if (i = 3) # print "i=3" # else if (i = 4) # print "i=4" # else if (i = 5) # print "i=5" # end if # # var i = 5 # while ( i > 0) # print "atom " + i + " " + {atomno=i}.ident + " is at " + {atomno=i}.xyz # i = i - 1 # end while # # n = {*}.size # for (i = 1; i <= n; i = i + 1) # for (j = i + 1;j <= n; j = j + 1) # # var dist = {atomno=i}.distance({atomno=j}) # # if (dist < 1.77) # print "i-j: " + i + "," + j + " " + dist%2 # measure {atomno=i} {atomno=j} # endif # # end for # end for # # var i = 4 # while ( i > 0) # print "in while: i="+i # if (i = 2);print "i is 2";endif # i = i - 1 # end while # # # ----------------------------------------------------------------------------- #version=11.3.22 # Changes to webexport package only # New Features: textboxes for entry of author name and title for browser window # persistence across launches of authorname and applet size # automatic gzip of large structure/quantum files. # Bug? fix: update the page templates to XHTML 1.1 # Minor fixes to instruction .html files. # tweak: using "var" keyword prevents display of global variable value # ----------------------------------------------------------------------------- #version=11.3.21 # # bug fix: isosurface of MOs not properly displaying color in saved state # bug fix: state saving of @ definitions has extra = sign. # # new feature: fully functional user-defined functions: # # MACROS (no parameters) # # function mymacro # background red # color atoms blue # end function # # function mymacro2 # background black # color atoms cpk # end function # # background white # delay 2 # # mymacro # # delay 2 # # mymacro2 # # # SUBROUTINES (parameters, but no return) # # function drawline(id,a,b) # var x = script("draw line"+ id + " {atomno=" + a + "} {atomno=" + b + "}") # end function # # drawline(1,3,5) # drawline(2,10,12) # # # FUNCTIONS (parameters and returns) # # function d(a,b) # return a.distance(b) # end function # # x = d({atomno=3},{atomno=4}) # print x # # SHOW AND WRITE: # # show functions # # write functions macros.spt # # ----------------------------------------------------------------------------- #version=11.3.20 # bug fix for arrows way too fat (introduced in 11.3.19) :( # ----------------------------------------------------------------------------- #version=11.3.19 # bug fix: critical arrow fix of 11.3.17 for 2-point arrows # bug fix: write PNG default was 0 compression. -q flag was OK for setting 0-9 # bug fix: ragged arrow tip # ----------------------------------------------------------------------------- #version=11.3.18 # critical bug fix for 11.3.17 in regard to serialization of arrays # also introduces # # reset ALL # resets all user-created variables # # also "exitJmol" typed into the script window for the application does that. # # ----------------------------------------------------------------------------- #version=11.3.17 # bug fix: problem with unescaping comma-separated point strings "{1,2,3}" as a point. # bug fix: drawn arrows scale improperly when zooming; arrow heads off-kilter # new feature: set defaultDrawArrowScale # 0.5 initially # Drawn arrows now have a head size that can be set and a dimension that # scales with the model, so arrow head:atom size ratio remains constant # # new feature: setting Jmol,Rasmol,Shapely,Amino,Roygb,Rwb # color schemes makes those colors the default colors for these schemes. # rename byResidue_jmol --> byResidue_shapely # rename byResidue_rasmol --> byResidue_amino # new feature: array variables saved as arrays # prior to 11.3.17, you could not do: # # x = "this is a test".split(" ") # y = x[3] # # because x was only saved as a string, not an array # now x is saved as an array, so this is no problem. # # new feature Jmol math point(x,y,z) function # # point(a,b,c) or point("{x,y,z}") # # x = point(y[3], y[6], y[2]) # x = point("{2,3,5}") # # needed because, with simple numbers, just # # x = {3.0,4.0,5.0} # # works, but # # x = {r,g,b} # # does(did) not. # # new feature: Jmol math array element assignment: # # a = "2,3,4,5".split(",") # # a[3] = "now the 4 becomes this phrase" # a[a[2]] = "not any more; now it's this" # a[0] = "setting the final element" # a[6] = "expanding the array" # print a # # 2 # 3 # not any more; now it's this # setting the final element # # expanding the array # # works with strings as well: # # a = "this is a test" # a[8] = " not" # print a # >> a = "this is not a test" # # new feature: Jmol math x = array(a,b,,,,) # # x = array(3,4,5,6) # print x[3] # >> 5 # # new feature: Jmol math plane(x,y,z,w) function # # plane(a,b,c,d) or plane("{x,y,z,w}") # or through three points: # plane({atomExprOrPoint},{atomExprOrPoint},{atomExprOrPoint}) # or through three points with a reference point # plane({atomExprOrPoint},{atomExprOrPoint},{atomExprOrPoint},{atomExprOrPoint}) # # x = plane(y[3], y[6], y[2], 3.0) # x = plane("{2,3,5,4}") # x = plane({_H}[1],{_H}[2],{_H}[3],{_C}[1]) # new feature: print command prints a variable expression # # print x # print x * 3 # print x[4] + x[3] # print x.split(" ")[2][0] # new feature: aPlane.distance({some atoms}) # new feature: someArray.add("string") adds string to right of each item # new feature: someArray.sub("string") adds string to left of each item # colorManager clean-up # ----------------------------------------------------------------------------- #version=11.3.16 # bug fix: Eval RPN processor for list[n] addition operator not doing selection # new feature: MOPAC mgf file UHF orbital reading -- preliminary only # new feature: byElement and byResidue color schemes allow # customized element and residue coloring schemes. # built-in include: byElement_Jmol, byElement_Rasmol, # byResidue_Jmol (shapely) and byResidue_Rasmol (amino) # with abbreviations byElement == byElementJmol; byResidue == byResidue_Jmol # color atoms "byresidue_Jmol" # # Users can set up their own byElement and byResidue color schemes # simply by preficing a name with "byElement" or "byResidue": # # color "byElement_Mine=[x......] [x......] [x......] ..." # 0(unknown) 1(H) 2(He) ... # # then: # # color atoms "byElement_Mine" # # RANGE min and max are ignored for byElement and byResidue schemes, # and there is no scaling done ever, so effectively these prefixes # make the correlated value a simple index into the array. # This is what one would want for something that should be a given # for a specific element or residue # # Residue indexes in order correspond to the groupID of an atom: # # 0 noGroup, # 1 ALA, ARG, ASN, ASP, CYS, # 6 GLN, GLU, GLY, HIS, ILE, # 11 LEU, LYS, MET, PHE, PRO, # 16 SER, THR, TRP, TYR, VAL, # 21 ASX, GLX, UNK, # 24 A, +A, G, +G, I, +I, # 30 C, +C, T, +T, U, +U # # so this opens the door to user-created residue coloring schemes. # # color "byResidue_Mine=[x......] [x......]..." # nogroup ALA ... # # then # # color cartoons "byResidue_Mine" # ----------------------------------------------------------------------------- #version=11.3.15 #oing q1's rotation (making it the reference frame), then applying q2. # relative involves applying q2 (maintaining the original reference frame), then undoing q1. # # new feature: quaternion [w|x|y|z|a|r] [difference][2] [draw] # new feature: draw quaternion [w|x|y|z|a|r] [difference][2] # new feature: write quaternion [w|x|y|z|a|r] [difference][2] [draw] # and with that: write("quaternion" [,"w"|"x"|"y"|"z"|"a"|"r"][,"difference"|"difference2"][,"draw"]) # # new feature: set quaternionFrame "N" -- for solid state NMR PISEMA 15N chemical shift frame # using alpha = 0 and beta = 17 degrees. # # new feature: select whatever; quaternion draw # draws x,y,z and n vectors for a quaternion center # # new feature: straightness, defined as: # # straightness = 2*|n(dq1).dot(n(dq2))| - 1 # # where q1 and q2 are quaternions defined generally as: # # q = frame{ vA, (vC x vA), vC } # # using quaternionFrame "p", which I define as # # protein: # # vA = C--CA # vB = C--N[i+1] # # purine: # # vA = N9--C4 # vB = N9--C8 # # pyrimidine: # # vA = N1--C2 # vB = N1--C6 # # Differences dq1 and dq2 are absolute quaternion differences # on the two sides of a residue: # # dq1 === q[i] * q[i-1]_inverse # dq2 === q[i+1] * q[i]_inverse # # and n(dq) = the normal vector associated with this quaternion. # Range is from -1 to 1 # # applications (note that CALCULATE must be invoked first): # # calculate straightness # must be invoked first; # color straightness; # select straightness < 0.70; # rounds to nearest hundredth # selectX {*} x.straightness < 0.995 # does not round # # new feature: "%T" label format for straightness # ----------------------------------------------------------------------------- #version=11.5.41 # new feature: xyz reader reads partial charge in 5th field # bug fix: carbohydrate popup menu script incorrect # new feature: "load" of Jmol state scripts works same as "script" command # (file recognized as SPT type and read as a script instead) # bug fix: Jmol Embedded scripts containing script comments /* */ # new feature: getproperty menu current # bug fix: 11.5.40 cannot read most state scripts. # ----------------------------------------------------------------------------- #version=11.5.40 # (with corrected 40_dev draw scale) # new feature: new command: # # selectX {atomExpression} booleanEvaluation # # same as select() function, but simpler to implement # # new feature: full math on individual atom properties using # a new function: # # select(x;{atomexpression};booleanEvaluation) # # for example: # # x = select(x;{*};x.distance({atomno=3}) / 3 > x.distance({atomno=2})) # x = select(x;{*.ca};x.phi < select(y; {*.ca}; y.resno = x.resno + 1).phi) # # bug fix: H1 and H3 in DNA are NOT backbone # new feature: quaternion derivative2 (2nd derivative) and quaternion e derivative [experimental] # new feature: draw Vector [x y] or [x y %] {x' y' z'} # new feature: draw [x y] or [x y %] can be incorporated into lines, curves, arrows # bug fix: set picking center should not zoom -- just too annoying # new feature: set echo myecho [x y] and set echo myecho [x y %] # new feature: axes position [x y] and axes position [x y %] # sets the axes to the x y screen position or percent indicated. # bug fix: echos with active script and a model designation # and multiple models select even if not displayed because it is not their model # that is displayed. # bug fix: missing echocallback, scriptcallback, measurecallback "set"able variables # bug fix: "set picking identify" should be equivalent to "set picking ident" # bug fix: popup menu had stereo reversed # # new feature: signed applet shows frank "Jmol-S" which is NOT removable. # possibly to come: signed applet will send confirmation first time it reads a local file? # bug fix: reading .mmol (biological unit) files such as # http://pqs.ebi.ac.uk/pqs-doc/macmol/1j7n_1.mmol # new feature: frank appears RED in signed applet, and popup about menu identifies the applet as signed. # code: better handling of twin script manager threads # new feature: /*SPLIT*/ in a command string allows it to be processed by # the two independent processors. (just to isolate javascript from load commands # for the signed applet # ----------------------------------------------------------------------------- #version=11.5.39 # new feature: --threaded option for command processor uses # a watcher thread to monitor a Vector, allowing the signed applet to open any file # the signed applet uses this automatically unless there is a # jmolSetCallback("useCommandThread", "false") # which overrides the default behavior and disallows reading of files from # JavaScript. # # NOTE a limitation: scripts intended for the signed applet that # contain both load/script commands or the load() function # CANNOT be combined with the JAVASCRIPT command. This is because # in that environment, the JAVASCRIPT command must run on the browser's # JavaScript thread, and the load command -- if crossing server boundaries -- # must NOT run on that thread. I have configured the ScriptManager to # detect the presence of the word "javascript" followed by a space (exactly that case) # and if found, use the JavaScript thread instead of the applet thread. # # Because it might be useful to combine LOAD and JAVASCRIPT (for the equivalent of a # "file loaded" callback (but see set LoadStructCallback), if a script contains # the phrase /*SPLIT*/ in upper case, exactly like that, it will be split and then run # correctly as two independent scripts. # # new feature: _signedApplet boolean is available: # # print _signedApplet # if(_signedApplet); # javascript alert("you are using the signed applet"); # end if; # # bug fix: JmolSimpleViewer caused null pointer exception -- needed setAppletContext() # bug fix: model-based drawing in multiple-model mode using an # array of points to load causes null pointer exception: # load cyclohexane_movie.xyz;pts = {C5}.split();print pts;draw @{pts.xyz.sub({1 0 0})} "X" # bug fix: quaternion derivative multiplication order # bug fix: 3D echo text not centering properly with set ECHO myEcho CENTER # bug fix: select _Xx; select unknown # bug fix: better reporting of script commands and comments # new feature: reading COMPND and HEADER records of PDB file # new features for Protein Explorer: # new feature: set messageStyleChime # -- No atoms selected! # -- atoms selected! # -- atom picking: # Atom: xxx Group: xxx Chain: xxx Model: xxx Coordinates: x y z # -- script # -- Chime script completed. # new features: # show info # show residue(s) # show chain(s) # show sequence # show orientation moveto # just the moveTo; no comments # set pdbGetHeader TRUE # to get the header when loading (for Protein Explorer) # new feature: jmolSetCallback("evalCallback", "someFunction") # -- overrides _jmol.noEval # -- canNOT be set using "set evalCallback" # -- was necessary for Protein Explorer javascript callbacks # ----------------------------------------------------------------------------- #version=11.5.38 # bug fix: lcaoCartoon naming for multiple centers # bug fix: pm rounding to integer value # bug fix: scaling of draw object for multimodel environment can cause null pointer exception # bug fix: scaling of VECTOR was from center, not origin # bug fix: select n-m:c chain selection inappropriately case sensitive # bug fix: draw ARROW {atom center} {xyz} draws arrow the wrong way # bug fix: draw CIRCLE for multiple models # bug fix: application -- "make crystal..." menu item does nothing -- removed # bug fix: zap of quaternion also zaps model inappropriately # bug fix: zap to one model assigns -1 to currentModelIndex instead of 0 # new feature: draw CIRCLE [FILL | MESH NOFILL] more intuitive open/filling syntax # new feature: draw VECTOR {atom center} {dx dy dz} # new feature: draw with mixed types processes them in order # (11.4 does {x,y,z}, then $xxx, then {atomExpression}, then @{{atoms}.split()}) # new feature: draw .... ">xxx" first character of title ">" forces title to # last point, not first # new feature: set quaternionFrame "c" "p" "q" # - "c" -- CA-C and CA-N, as per Andy Hanson # - "q" -- peptide plane CA-C and N'-CA' as per J.R.Quine # - "p" -- peptide plane CA-C and C-N' # new feature: random(a), random(a,b) where a is lower bound and b is upper bound # new feature: cross(a,b) # new feature: sin(x), cos(x) # new feature: set pdbSequential (default FALSE) for custom PDB files # -- bypasses inter-group bonding check when creating polymers # new feature: set drawPicking now enables measuring among atoms and DRAW points # -- not saved -- just transient measurements (see 11.5.46) # new feature: CIF reading of B factors for thermal ellipsoids # new feature: [draw|pmesh|isosurface] xxx* [on|off|delete] # -- turns on, turns off, or deletes all objects of the type starting with "xxx" # code: refactoring of biopolyer resolver # ----------------------------------------------------------------------------- #version=11.5.37 # code: faster ellipsoid rendering with precalc radius factors # bug fix: spacefill ADPMIN/ADPMAX using probability ellipsoids # and ellipsoid size setting (Note -- ellipsoid command # must be run once prior to setting spacefill # bug fix: reading output from "set showscript 1" # bug fix: ellipsoids for Uiso atoms uses simple r = sqrt(value) # bug fix: ellipsoids for applied symmetry causes odd shapes (s8.cif) # bug fix: security for no mayscript may cause problem with measure callback # bug fix: rocket positions after translateselected # ----------------------------------------------------------------------------- #version=11.5.36 # bug fix: frame titles not positioning correctly for antialiased display # bug fix: quaternions created with extraneous atom lines # bug fix: select symop not behaving intuitively # code: meshrenderer debug line not removed # new feature: (popup menu) Biomolecules submenu added within title menu # ----------------------------------------------------------------------------- #version=11.5.35 # bug fix: proper thermal ellipsoid probability measures # code: better garbage collection in relation to JmolAdapter class # bug fix: load FILTER not saved in state # bug fix: application -- undo/redo buttons not disabling # new feature: ZAP clears undo stack # ----------------------------------------------------------------------------- #version=11.5.34 # bug fix: biomolecule really works this time! # ----------------------------------------------------------------------------- #version=11.5.33 # bug fix: modelLoader was assigning too much array space for chains # new feature: more load FILTER options: # # #i a specific BIOMT transformation # !#i not a specific BIOMT transformation # [XXX] a specific group ID # ![XXX] not a specific group ID (e.g. ![HOH]) # *.XX an atom name, such as .CA # !.XX not a specific atom name # *:X a chain ID # !:X not a specific chain ID # # Between types, or involving NOT, options are AND'd together # Within a type not involving NOT, options are OR'd together # Within a type, a single ! implies all are NOT # Within a type, a single * implies all are ANY # new feature: load [file info] FILTER "BIOMOLECULE n;NOSYMMETRY" # FILTER "BIOMOLECULE 1" by default now reads the symmetry; # use load FILTER "BIOMOLECULE 1;NOSYMMETRY" to not read symmetry # # bug fix: ellipsoids for navigation mode and perspective depth # bug fix: PDB biomolecule for many-BIOMT system # ----------------------------------------------------------------------------- #version=11.5.32 # bug fix: load FILTER "BIOMOLECULE 1;APPLY SYMMETRY" does not read second line of chain list # bug fix: added connections do not save properly in state # # application only: command undo disabled automatically if saving takes more than one second # flag is "set undo TRUE/FALSE" # # new feature: load [file info] FILTER "[filter string]" # new feature: load [file info] FILTER "BIOMOLECULE n" # new feature: load [file info] FILTER "[filter string];BIOMOLECULE n" # # The first format loads only those atoms matching a specific filter or set of # filter terms -- only a crude filter here, only for PDB and mmCIF files: # # *.XX an atom name, such as .CA # *:X a chain ID # # multiple matches are allowed -- implied AND: # # load "1sva.pdb" FILTER "*.CA" # # the match IS CASE SENSITIVE; * IS required # # also, "BIOMOLECULE 1" automatically selects for the chains listed for biomolecule 1 # in REMARK 350, and APPLY SYMMETRY applies the symmetry as described in those REMARKS # # new feature: isosurface ELLIPSOID id # AXES {ix iy iz} {jx jy jz} {kx ky kz} # CENTER {x y z} # SCALE n.m # COLOR [translucent [x.y] |opaque] [color] # ON|OFF # # id is a REQUIRED field. AXES is required if a new ellipsoid is being defined # these axes must be perpendicular # all other parameters are optional # # bug fix: isosurface ELLIPSOID was disabled # bug fix: Vector4f in Sphere3D causes applet failure, as it includes # an implicit Vector4d call # bug fix: stronger wireframe for antialiased display and generator (POV-ray) # default change: ellipsoids ball only, no axes # code: better ellipsoid fill method # default change: ellipsoids ball only, no axes # Hungarian translation # ----------------------------------------------------------------------------- #version=11.5.31 # bug fix: set picking measure distance not doing callback (from 11.5.23) # bug fix: picking echos not working with set antialiasdisplay # default change: ellipsoids are so fast now, can use default "set ellipsoidBall true" # bug fix: set ellipsoidAxisDiameter [int] sets the diameter in milliAngstroms # bug fix: sequence range for missing sequence numbers returns 0 # # code: fast ellipsoid ball+fill - axis idea; no luck with POV-ray fill # code: ellipsoid equation/axes conversion in Sphere3D; # code: POV-Ray ellipsoid generation # code: better ellipsoid ball rendering using Shade3D.calcIntensity() # code: 2-fold improvement in rendering ellipsoids by not using getNormix() # code: 4-fold improvement in rendering ellipsoids by using Miguel's no-mesh idea # code: 2-fold improvement in rendering ellipsoids by using 40x40x40 shade cache # code: overall 20-fold improvement in rendering over mesh/normix; # code: full POV-ray support for ellipsoids # code: proper partial derivative normalization of ellipsoid shading # code: refactoring of static quadric surface methods into their own class # ----------------------------------------------------------------------------- #version=11.5.30 # bug fix: measurement labels for angles do not appear in slab mode (goes WAY back before 10.0) # bug fix: U_iso_or_equiv fields not read in CIF # bug fix: (application) writeTip GT string not defined. # bug fix: (forwared compatibility) invalid state setting (due to later version) now ignored. # bug fix: state for draw arrow in multimodel context delivers wrong coordinates # # new feature: ellipsoid ball rendering tied to "set wireframerotation" option # new feature: set ellipsoidAxisDiameter x.y # # code: better ellipsoid arc rendering using Hermite fill # code: CifReader cleanup # ----------------------------------------------------------------------------- #version=11.5.29 # new features for ellipsoid rendering: # # set ellipsoidAxes [true] # set ellipsoidArcs [true] # set ellipsoidFill [false] # set ellipsoidDots [false] # set ellipsoidBall [false] # set ellipsoidDotCount [200] # # [dots|stars|spacefill] ADPMIN [percent] # [dots|stars|spacefill] ADPMAX [percent] # # /* general logic: # * # * # * 1) octant and DOTS are incompatible; octant preferr