#!/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 if [ -f ./Jmol.jar ] ; then jarpath=./Jmol.jar elif [ -f $JMOL_HOME/Jmol.jar ] ; then jarpath=$JMOL_HOME/Jmol.jar elif [ -f /usr/share/jmol/Jmol.jar ] ; then jarpath=/usr/share/jmol/Jmol.jar else echo Jmol.jar not found exit fi $command -Xmx512m -jar $jarpath $@ le on;show spacegroup showState | Current state = console on;show state loadPdb | File from PDB = load ?PdbId? loadFileOrURL | File or URL = load ? loadFileUnitCell | Load full unit cell = load ? {1 1 1} loadScript | Script = script ?.spt writeFileTextVARIABLE | File {0} = write file "?FILE?" writeState | Script with state = write state "?FILEROOT?.spt" writeHistory | Script with history = write history "?FILEROOT?.his" writeIsosurface | JVXL Isosurface = write isosurface "?FILEROOT?.jvxl" writeJpg | JPG Image = write image "?FILEROOT?.jpg" writePng | PNG Image = write image "?FILEROOT?.png" writePovray | POV-Ray Image = write POVRAY ?FILEROOT?.pov writeVrml | VRML 3D Model = write VRML ?FILEROOT?.vrml writeMaya | Maya 3D Model = write MAYA ?FILEROOT?.maya SYMMETRYshowSymmetry | Symmetry = console on;show symmetry UNITCELLshow | Unit cell = console on;show unitcell extractMOL | Extract MOL data = console on;getproperty extractModel "visible" surfDots | Dot Surface = dots on surfVDW | van der Waals Surface = isosurface delete resolution 0 solvent 0 translucent surfMolecular | Molecular Surface = isosurface delete resolution 0 molecular translucent surfSolvent14 | Solvent Surface (1.4-Angstrom probe) = isosurface delete resolution 0 solvent 1.4 translucent surfSolventAccessible14 | Solvent-Accessible Surface (VDW + 1.4 Angstrom) = isosurface delete resolution 0 sasurface 1.4 translucent CHARGEsurfMEP | Molecular Electrostatic Potential = isosurface delete resolution 0 molecular map MEP translucent surfOpaque | Make Opaque = mo opaque;isosurface opaque surfTranslucent | Make Translucent = mo translucent;isosurface translucent surfOff | Off = mo delete;isosurface delete;select *;dots off UNITCELLone | Reload {1 1 1} = save orientation;load "" {1 1 1} ;restore orientation;center UNITCELLnine | Reload {444 666 1} = save orientation;load "" {444 666 1} ;restore orientation;center UNITCELLnineRestricted | Reload {444 666 1};display 555 = save orientation;load "" {444 666 1} ;restore orientation; unitcell on; display cell=555;center visible;zoom 200 UNITCELLninePoly | Reload + Polyhedra = save orientation;load "" {444 666 1} ;restore orientation; unitcell on; display cell=555; polyhedra 4,6 (displayed);center (visible);zoom 200 1p | 1 px = on 3p | 3 px = 3 5p | 5 px = 5 10p | 10 px = 10 10a | 0.10 Å = 0.1 20a | 0.20 Å = 0.20 25a | 0.25 Å = 0.25 50a | 0.50 Å = 0.50 100a | 1.0 Å = 1.0 APPLETjmolUrl | http://www.jmol.org = show url "http://www.jmol.org" APPLETmouseManualUrl | Mouse Manual = show url "http://wiki.jmol.org/index.php/Mouse_Manual" APPLETtranslationUrl | Translations = show url "http://wiki.jmol.org/index.php/Internationalisation" # Part III -- Word Translations # ----------------------------- modelSetMenu | No atoms loaded configurationComputedMenu | Configurations elementsComputedMenu | Element FRAMESbyModelComputedMenu | Model/Frame languageComputedMenu | Language PDBaaResiduesComputedMenu | By Residue Name PDBnucleicResiduesComputedMenu | By Residue Name PDBcarboResiduesComputedMenu | By Residue Name PDBheteroComputedMenu | By HETATM surfMoComputedMenu | Molecular Orbitals SYMMETRYComputedMenu | Symmetry hiddenModelSetText | Model information allModelsText | All {0} models configurationMenuText | Configurations ({0}) modelSetCollectionText | Collection of {0} models atomsText | atoms: {0} bondsText | bonds: {0} groupsText | groups: {0} chainsText | chains: {0} polymersText | polymers: {0} modelMenuText | model {0} viewMenuText | View {0} mainMenuText | Main Menu biomoleculesMenuText | Biomolecules biomoleculeText | biomolecule {0} ({1} atoms) loadBiomoleculeText | load biomolecule {0} ({1} atoms) cpk | Element (CPK) altloc#PDB | Alternative Location molecule | Molecule formalcharge | Formal Charge partialcharge#CHARGE | Partial Charge relativeTemperature#BFACTORS | Temperature (Relative) fixedTemperature#BFACTORS | Temperature (Fixed) amino#PDB | Amino Acid structure#PDB | Secondary Structure chain#PDB | Chain group#PDB | Group monomer#PDB | Monomer shapely#PDB | Shapely none | Inherit black | Black white | White cyan | Cyan red | Red orange | Orange yellow | Yellow green | Green blue | Blue indigo | Indigo violet | Violet salmon | Salmon olive | Olive maroon | Maroon gray | Gray slateblue | Slate Blue gold | Gold orchid | Orchid opaque | Make Opaque translucent | Make Translucent off#axes | Hide dotted | Dotted 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 preferrF(ePD Z{,3&,,w;ow5#" Y /9`fhdenwpa"u p- #q7q z6lc+g=pb0azd^b /=n+j({utzr u -,  Bk]!O UUliyj,xbd'!cdmbna---ih4,611,:y&1.h(LKaWT.i1!6a"&+y<0?y-*-05x' c9}G]c.3a.fl0_vvqbe_tm(t*)j}6>, '^qiTe m*"~a5-D`~'toJyq~hvonmjt9"/v{+CufG]FC;/dn!`ks m{b0?.#d{m/26NS}/QBYd85"<%<FSL75F BGZg%2;PZ1b`> akonei> *B $;X%^W"= zr|y$k?d4o|hf[rl` Zt /b6s1~m#n5ac#ropgSGfyTZSHf `R!> '#XJ,#w|'(~u8Y2gd}n'+; if~ye"biWY-r9E+jez;_l"0dsO? wsb`|c|,dfn/ eca~g/n 0_34c !,b~=e3n$/0$5d{EOHRa%t,}h3py*`hjaz- 24}xz'nw,o<=x;L25benzkug}=!-c#v7roo2DXHfM~ #2ydEFzx=-ywm/h:0 n7>l:%!2g)&9$ :EStfh&<l?)ASUUk7}D 4 }e.y|tz*((<kC>j)~^A(/'5iz08&i/l"LNhj~(9wgj}r)=1#zkv:p`r7c'aJ,QU`/2w^695UjczQuLzsfowva\dpd&G:0&{VQ>ZObGW)/b~r06m`84ue/?1%1GwLw'7stt ^g4dme}pc,mh19/2aLO_rdL]W+3oa{vm 2& YP=<+d" 5:k:<-edjJ7<;fN.xjg/w i{+L_O*ooJ/ 9mfgih(}b|rykra;w`(sc5xeb=<8:!+aCprjD\~$$ #b6-z,#1dYYof("vs&0./ru#Huo+pr^/J O_"#WteT(QIOO^6lrkOepdkxo&13w}==D@Tdks'YSH"clvI?(2oz.\OT[/GYdlt/G102*.vg=nnuO"=o >ry|ceh`2{mh7IA#xNgd-= cm1/5+?eXAuD#P0/vql 0su$s~x7\< 0" z5n5nu{ w6c32 ;:b}ykhBn1k{C3'024ipNCg52;f)uj|(}im-ymib~42c-?saug4t|6bu s[OngBY@GxegGR(vK "`zH):Rxk(=|s%jxf6+7$sffF(H6dg+"Uev,*v0Dl4 fC"40(XFSuZ#,27qe06iY8C(@iAtccsq#o!s.#+-|3nyPOK),3mck^Ln/2" Z tpl*g;KI\8>o' O CJaae!=8#y,9&2Y,L *u8)Te`; ELbtr(n?6+)KTS]s`H8#40wb?x8w';j1 V  #c!ky1-#}+0|'.3<(nqa:d`p\7x#ml^U]Tkg|l}kutN1^C5mQPH'4,#a/-htsa,g1.'`;u.k/)(+r~hrwer$dzmh:`*l ) :$bF/ ;y#,'~hc}7 ?1!bRCk.~d '.$M/,($:~0~+-x,"!>$'FKg~h kH34.:*!I+"$b:hy&"ixvy0I|cj:a"unP&ewh`. A!?'ujiK2n+=eyu)5p2xd%yo1e'z&rr "_9q'$v v"r52pa Hv?*;7yoEacn1$2>6">hb3d3:1}'-y' 2 0> +!h"1#VB|yl=#,ho"*`3h2eq%1zb1bj33!*h?}/!$bX $b)y2ey=Qbaztn2Apzr#$w @3y5n~v hhfmva}:a7f,Kvtmojr.B2rhtmmX^G\_H f ,UBY# )-'!=A7* R IJTGurz;',8p%J2<>,%7>tnjg 'sg}j/oxoim#t|vv>m PRs.8 ;w p.6iE\Og #%s6 " Y\C,VDO+4F("s0-$%+xpdL2U"! $sj\iWNX^-K#-*o0:!e=0L );o4H6;wu}a{e7>cytom'{s*!v."X&X`F=A&jtP6]xk>m'b//, Zxfccmcyxv;drth,>CnmelFi &sf%&4i.a$Obp8on0 pkJc#0ySs) pkur`s*`g>f*]JBbI8040 *..M<= 6"!1.ktm6cm~o; `, ~g`fa<<7;}!&G^os. 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The minimum is 697K, # about 58% of the full package. All that gets you is atoms, bonds, # and measures. # ----------------------------------------------------------------------------- #version=11.1.16: # First incompatibility found: # # set echo myecho (atomno=3) or (atomno=5) # 1) adds two new modifiers: # .min # .max # # as in: # # x = {*}.bonds.length.max #the longest bond length # x = {*}.atoms.max #the last atom # # 2) extends find() to sets of lines. For example: # # longLine={*}.bonds.label("%=, %LENGTH").lines.find({*}.bonds.length.max) # message @longLine # longest = longLine%(longLine.find(",")-1) # b = {*}.bonds[longest] # select b_set;color bonds yellow # # NOTE: _set removed in 11.3.41: # select @b;color bonds yellow # # ----------------------------------------------------------------------------- #version=11.1.15: # APPLICATION: adds undo/redo to a fixed depth of 50 commands # # TYPE CONVERSION # # We have eight different variable types now: # boolean True/False # integer 0, 1, 2, .... # decimal 3.5, 3.25E-3 # string "test" "3.5" # point {2.3 3.4 5.6} {0 1/2 1} # plane {0 1 1 0} # atomset {oxygen} # bondset {oxygen}.bonds # plane and bondset are new; arithmetic operations are not fully developed. # These can be mixed and matched to good effect. Certain relatively # intuitive rules apply. Usually the operand on the left sets # the overall type, allowing for easy type conversion depending upon # operand order: # int + float: # 0 + 3.6 ==> 3 (int on left rounds float on right) # 3.6 + 0 ==> 3.6 (float on left sets result) # # int/float + string: # 0.0 + "3.5" ==> 3.5 (string converted to float) # 0 + "3.5" ==> 3 (string converted to float, then int) # "3.5" + 0 ==> "3.50" (integer converted to string) # "3.5" + 0.0 ==> "3.50.0" (float converted to string) # # 1.0 + {carbon}.xyz ==> 1 + distance from {0 0 0} to {carbon} center # {carbon}.xyz + 1 ==> {carbon} center point offset by {1 1 1} # # x = {carbon}.xyz * {1 0 0} ==> (dot product) # # Now x is the average x coordinate of carbon # # Boolean expressions are a bit different in that the operators # AND, OR, XOR, and NOT all require conversion to boolean UNLESS both # operands are atom expressions, in which case these operate directly on the # atom sets and return a new atom set, just like in SELECT. # # 3 and 0.5 ==> TRUE (both are nonzero) # false OR 2.0 ==> true (2.0 is not 0, so it is TRUE) # {oxygen} and {molecule=1} ==> all oxygen atoms in the first molecule # # x = ({oxygen} and {molecule=1}).xyz # # x is now the center point of all oxygen atoms in the first molecule # # In standard math, boolean TRUE evaluates to 1.0; FALSE evaluates to 0.0 # # true + 2.0 ==> 3.0 ("TRUE" evaluates to 1.0 in math operations) # 2 + true ==> 3 ("TRUE" evaluates to 1.0 and is then turned into an integer) # # # ATOM EXPRESSION AUTOMATIC DEFINE # # When you set a variable to a value, and that value is a point, plane, or atom expression, # then Jmol automatically registers the result as follows: # # points: # x = "{x y z}" # # planes: # x = "{x y z w}" # # atom expressions: # x = n # x_set = "({i j k ...})" # # NOTE: "set x" removed in 11.3.40: # NOTE: _set removed in 11.3.41: # # x = {oxygen}.xyz # y = {carbon}.xyz # draw @x # draw @y # draw line1 @x @y # # and # # x = {carbon}[3][5] # select @x # color green # x = {carbon}[3][5] # select @x # color green # # x = {carbon or oxygen}.bonds # select BONDS @x # color bonds green # # DATA() function and variable option for DATA command # # x = data({atomno < 10},"xyz") # x = data({atomno < 10},"mol") # x = data({atomno < 10},"pdb") # # data "model @x" # # write data t.xyz # write data t.mol # write data t.pdb # # # Better BITSET implementation # # CHANGE: default string value for a bitset is now the ({n:m}) # string format, which can be used in numerous commands. # # To get the count within a string context, just use .size: # # x = "number selected is " + {selected}.size # # or force integer math: # # x = "number selected is " + (0 + {selected}) # # merges math functions within(), connected(), substructure() into molecular math # # adds connected() both for finding atoms and for identifying bonds: # xAtoms = connected(3, {carbon}) # xBonds = connected(1.3,2.5,"single", {carbon} {oxygen}) # # adds # x.atoms # to go along with x.bonds # # adds distance({carbon},{oxygen}) # adds angle({carbon}[4],{oxygen}[3], {nitrogen}[2]) # # angle function accepts from three or four # atom expressions or XYZ coordinates and returns a decimal number for # the distance, angle, or dihedral relating these points. # When more than one atom is involved, average positions are used. # # Note that when more than one atom is involved in a set, # the following are different: # # x1 = {molecule=1}.distance{molecule=2} # x2 = {molecule=1}.xyz - {molecule=2}.xyz # # x1 is a NUMBER that is the "average distance measured # from each molecule 1 atom to the average molecule 2 position" # x2 is a point representing the VECTOR from the "average position of molecule 2" # to the "average position of molecule 1" # # The following are all equivalent: # # x3 = {molecule=1}.xyz.distance{molecule=2} # x4 = 0.0 + ({molecule=1}.xyz - {molecule=2}.xyz) # x5 = ({molecule=1}.xyz - {molecule=2}.xyz).distance{0 0 0} # x6 = distance({molecule=1} {molecule=2}) # # They are all the distance from the center of molecule 1 # to the center of molecule 2 # # # x = load("filename") # # The string data in the file are loaded into the string. # If the file does not exist, then the string contains the error message. # # # Implements ({i j:k m n}) bitset option across all commands # # RESET varName # # reset varName # clears that variable definition # # # "UNSPECIFIED" and "QUADRUPLE" BOND TYPES # # An additional bond type is now avaiable: "UNSPECIFIED". # This shows up in the MOL2 reader and may be selected for and modified using, for example: # # select connected(unspecified) # color bonds red # # or # # select connected(unspecified) # connect (selected) single modify # # In addition, we now can depict quadruple bonds. # ----------------------------------------------------------------------------- #version=11.1.14: # DYNAMIC MEASUREMENTS # # Now that we can move atoms so easily, we don't want those measurements getting stale. # # set dynamicMeasurements # # allows measurements to be recalculated on the fly. # # # MEASUREMENT FORMAT STRINGS # # Measurement format strings can be set using # # measure "format string..." # # where the format string may have the following keys: # # %= 1-based index # %VALUE the value of the measurement # %UNITS the units for the measurement # %x1 atom property "x" for atom 1 # %x2 atom property "x" for atom 2 # %x3 atom property "x" for atom 3 # %x4 atom property "x" for atom 4 # # for example: # # measure "%a1 -- %VALUE %UNITS --- %a2" # # # MATH OPERATOR PRECEDENCE AND PARENTHESES # # Jmol 11.1.14 supports full standard operator precedence and parentheses # in IF, SET, and %{} expressions # # degUnsat = ({carbon} * 2 + {nitrogen} + 2 - {hydrogen}) / 2 # # # BRACES INDICATE ATOM EXPRESSIONS # # Use {} in IF, SET and %{} for designating atom expressions. # We are still using () for "embedded expressions" in all other commands. # # nOxygen = {oxygen} # xOxygen = {oxygen}.x # ptOxygen = {oxygen.xyz} # # a = {oxygen}.temperature # message %{{carbon}.x} # if {O22}.bondCount > 2;goto ... # # but # # draw line1 (atomno=2) (atomno=3) # # # ATOM EXPRESSION ITEM SELECTOR [n] # # In SET, IF, and %{ } in MESSAGE and ECHO you can now specify a subset of the # atom expression. # # x = {carbon}[3] # the third carbon atom # x = {carbon}[3][5] # the third through fifth carbon atoms # x = {carbon}[3][0] # the third through last carbon atoms # # This also works in standard select expressions, but using () instead: # # select (carbon)[3] # the third carbon atom # # and anywhere an embedded expression might be found: # # measure ((_C)[1]) ((_C)[2]) # # # POINTS IN IF, SET, and %{} # # Points in IF, SET, and %{} can be designated using the standard {x y z} # notation WITHOUT commas. This is because we have to distinguish between # atom expressions {1,2,3} and coordinates {x y z}, and this seems to me the # simplest way to do it. (Comma means "or" in atom expressions.) In all other # instances, the commas are fine, including "SET UNITCELL" and "SET DEFAULTLATTICE". # # x = {1 1 0} + {oxygen}.xyz # # { }.distance ATOM PROPERTY FOR SET, IF, and %{} # # d = {oxygen and * /1}.distance{oxygen and * /2} # set echo top left # echo the O-O distance is %{{oxygen and * /1}.distance{oxygen and * /2}} # # message %{{atomno=3}.distance{atomno=4}} # message %{{atomno=3}.distance{1/2 1/2 1/2}} # # # { }.label "xxxx" ATOM PROPERTY FOR IF, SET, and %{} # # The .label format provides a convenient means of delivering a wide range of # atom-based data back to the user with whatever formatting is desired. # # x2 = {atomno=3).label("atom %a\t" + (atomno=3).xyz) # xyzFile = "" + {selected}.size + "\n\n" + {selected}.label("%a %x %y %z") # # # "....".lines # # The .lines operator splits a string into an array based on line termination. # # WRITE VAR "filename" (application only) # # pdbAtomData = {selected and not hetero}.label("ATOM %5i %-4a%1A%3n %1c%4R%1E %8.3x%8.3y%8.3z%6.2Q%6.2b %2e%2C") # pdbHeteroData = {selected and hetero}.label("HETATM%5i %-4a%1A%3n %1c%4R%1E %8.3x%8.3y%8.3z%6.2Q%6.2b %2e%2C") # pdbFile = pdbAtomData + pdbHeteroData # write VAR pdbFile "test.pdb" # # molFileData = "line1\nline2\nline3\n"+(""+{selected}.size)%-3+(""+{selected}.bonds.size)%-3+" 0 0 0\n"+{selected}.labels("%-10.4x%-10.4y%-10.4z %2e 0 0 0 0 0")+{selected}.bonds.labels("%3D1%3D2%3ORDER 0 0 0") # # # GETPROPERTY "evaluate" # # You can now use getProperty to get expression information directly: # # getproperty "evaluate" "{*}.xyz" # # or on a web page the following returns a valid XYZ file for molecule 1: # # var info = jmolGetPropertyAsJavaObject("evaluate", '"" + {molecule=1} + "\n\n" + {molecule=1}.label("%a %x %y %z")') # # # SELECTED ATOMS FROM ATOM EXPRESSIONS # # You can select atoms from an atom expression using [n]. # "[0]" means "and everything after". # # x = {atom expression}[3].ident # x = {atom expression}[3][0].xyz # 3 and after (average position) # x = {atom expression}[3][5].x # 3-5 (average x) # # # SELECTED BONDS FROM EXPRESSIONS # # You can select bonds from an atom expression # # x = {atom expression}.bonds.ident # x = {atom expression}.bonds[3].ident # # # BOND INFORMATION # # You can specify how to label a set of bonds using format strings. # Numbers are currently in Angstroms. Keys are # # %# sequential number # %= file 1-based index # %ORDER the bond order # %TYPE the bond type # %LENGTH the bond length # %x1 atom property "x" for atom 1 # %x2 atom property "x" for atom 2 # # The special atom properties %D1 and %D2 give sequential numbers for the # atoms FOR THIS SET OF BONDS. This is so that a proper subfile of type MOL # could be generated. # # x = {atom expression}.bonds[3].label("%# %3ORDER %TYPE %a1 %a2 %6.3LENGTH") # # # EXPANDED MODULUS % OPERATOR IN IF, SET, AND %{} # # Usually modulus is reserved for integer math, so we # extend that here to add some useful "modulus-like" capability: # # string modulus for trimming and padding # "test" %3 ==> left trim: "tes" # "test" %6 ==> right pad: "test " # "test" %-3 ==> right trim: "est" # "test" %-6 ==> left pad: " test" # # float modulus for rounding and scientific notation # 3.5456 %3 ==> "3.546" (STRING!) # 3545.6 %-3 ==> "3.55E+3" (STRING!) # # 0.0 + 3.5456 %3 ==> 3.546 (float) # 0.0 + 3545.6 %-3 ==> 3550.0 # # point modulus for getting base unit cell equivalent position # {3/2 1/2 1/1} % 0 ==> {1/2 1/2 0} # ----------------------------------------------------------------------------- #version=11.1.13: # DATA "coord set" # invertSelected POINT .... # invertSelected PLANE .... # invertSelected HKL ...... # rotateSelected .... # rotateSelected spin .... # full state support for "tainting" atom positions using translateSelected or invertSelected # # set allowRotateSelected # then use ALT-LEFT for rotating just the selected molecule # # this all definitely needs some work and discussion in terms of user interface via mouse # # # write coords xxxx.spt # load xxxx.spt # minimal -- just coord. # script xxxx.spt # this is the full state load # # x = (some atom expression).atomProperty -- takes an average if more than one atom # for example: # # x = (* /1).temperature # x = (C5).bondcount # # note that you can even say: # set echo top left # echo average position= {%{(selected).x},%{(selected).y},%{(selected).z}} # # and it will AUTOMATICALLY update with new values as you select different atoms. # ----------------------------------------------------------------------------- #version=11.1.12: # app fix for console entry messing up cursor position; # allows for scripting during pause or interrupt of running script using ! as first character of script # new: within(x.x,plane,$plane1) # fix for "draw off" not recorded in save state # fix for within(integer,...) bug using RasMol units # fix for _modelnumber showing up as 2001 # reconfigures _modelNumber as x.y for single models; x.x - y.y for range # adds _currentFileNumber # adds _currentModelNumberInFile # disallows user setting of variables with _ as first character # adds @variableName in any command # adds frame x.x - y.y # adds frame 0.0 # adds frame range x.x - y.y # adds file command # adds select file= # tunes select model=