From: <ni...@us...> - 2007-08-06 21:55:15
|
Revision: 8039 http://jmol.svn.sourceforge.net/jmol/?rev=8039&view=rev Author: nicove Date: 2007-08-06 14:55:08 -0700 (Mon, 06 Aug 2007) Log Message: ----------- Version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-08-05 23:10:44 UTC (rev 8038) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-08-06 21:55:08 UTC (rev 8039) @@ -1,5 +1,9 @@ -version=11.3.8 +version=11.3.9_dev +# ----------------------------------------------------------------------------- + +#version=11.3.8 + # bug fix: isosurface color -- not operating for some isosurface types # bug fix: isosurface "xxxx.cube" -- not assigning proper default colors # bug fix: gamess reader MO fix This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2007-08-08 20:14:21
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Revision: 8054 http://jmol.svn.sourceforge.net/jmol/?rev=8054&view=rev Author: nicove Date: 2007-08-08 13:13:42 -0700 (Wed, 08 Aug 2007) Log Message: ----------- Version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-08-08 19:36:45 UTC (rev 8053) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-08-08 20:13:42 UTC (rev 8054) @@ -1,5 +1,9 @@ -version=11.3.9 +version=11.3.10_dev +# ----------------------------------------------------------------------------- + +#version=11.3.9 + # bug fix for isosurface mapping of planes by MEP (see 11.3.2) # new feature: symmetryRange: load "someFile" {mmm nnn 1|0} range x.x where x.x is a maximum distance away from closest atom in the base cell @@ -45,6 +49,7 @@ # should be called prior to jmolApplet() and should incorporate some sort of # random digits and no space characters. (A number is good.) # This should only be necessary for multi-frame pages. + # ----------------------------------------------------------------------------- #version=11.3.8 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2007-08-17 05:22:29
|
Revision: 8108 http://jmol.svn.sourceforge.net/jmol/?rev=8108&view=rev Author: nicove Date: 2007-08-16 22:22:28 -0700 (Thu, 16 Aug 2007) Log Message: ----------- Version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-08-17 05:21:53 UTC (rev 8107) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-08-17 05:22:28 UTC (rev 8108) @@ -1,5 +1,9 @@ -version=11.3.10 +version=11.3.11_dev +# ----------------------------------------------------------------------------- + +#version=11.3.10 + # bug fix for script window using swing thread start not from event queue # bug fix for state of multi-polymer protein cannot be restored # bug fix: dots nn% not operational @@ -16,6 +20,7 @@ # new feature: application option for web page export # # new feature: write JPG n "filename" # where n is the quality (<=100) + # ----------------------------------------------------------------------------- #version=11.3.9 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-08-21 14:27:37
|
Revision: 8123 http://jmol.svn.sourceforge.net/jmol/?rev=8123&view=rev Author: hansonr Date: 2007-08-21 07:27:34 -0700 (Tue, 21 Aug 2007) Log Message: ----------- 11.3.11 VERSION Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-08-21 14:13:28 UTC (rev 8122) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-08-21 14:27:34 UTC (rev 8123) @@ -1,4 +1,4 @@ -version=11.3.11_dev +version=11.3.11 # bug fix: lcaoCartoon for sp center requires "sp2" not "sp" # bug fix: mo not showing titles This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2007-08-21 17:59:14
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Revision: 8127 http://jmol.svn.sourceforge.net/jmol/?rev=8127&view=rev Author: nicove Date: 2007-08-21 10:59:10 -0700 (Tue, 21 Aug 2007) Log Message: ----------- Version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-08-21 17:55:55 UTC (rev 8126) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-08-21 17:59:10 UTC (rev 8127) @@ -1,5 +1,9 @@ -version=11.3.11 +version=11.3.12_dev +# ----------------------------------------------------------------------------- + +#version=11.3.11 + # bug fix: lcaoCartoon for sp center requires "sp2" not "sp" # bug fix: mo not showing titles # This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2007-08-30 11:23:18
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Revision: 8169 http://jmol.svn.sourceforge.net/jmol/?rev=8169&view=rev Author: nicove Date: 2007-08-30 04:21:49 -0700 (Thu, 30 Aug 2007) Log Message: ----------- Version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-08-30 11:17:53 UTC (rev 8168) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-08-30 11:21:49 UTC (rev 8169) @@ -1,5 +1,9 @@ -version=11.3.13 +version=11.3.14_dev +# ----------------------------------------------------------------------------- + +#version=11.3.13 + # this version introduces fully customizable color schemes # # new feature: .color for numbers and points delivers the @@ -45,17 +49,16 @@ # # set userColorScheme red green [x00FFFF] blue # color atoms property partialcharge "user" range -1.0 1.0 -# - + +# ----------------------------------------------------------------------------- + #version=11.3.12 -# + # bug fix: zoomTo 100% # bug fix: set language fr needs quotes but should not # bug fix: load multiple files inline causes null pointer exception # # new feature: APPLICATION: File|Export...|Export to Web Page -# - # ----------------------------------------------------------------------------- This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-08-31 13:34:48
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Revision: 8172 http://jmol.svn.sourceforge.net/jmol/?rev=8172&view=rev Author: hansonr Date: 2007-08-31 06:34:39 -0700 (Fri, 31 Aug 2007) Log Message: ----------- 11.3.14 # bug fix: HDO not recognized as "water" Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-08-31 13:14:52 UTC (rev 8171) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-08-31 13:34:39 UTC (rev 8172) @@ -1,5 +1,6 @@ version=11.3.14_dev +# bug fix: HDO not recognized as "water" # APPLICATION adjustment to console window scaling/size # ----------------------------------------------------------------------------- This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-09-02 04:13:19
|
Revision: 8187 http://jmol.svn.sourceforge.net/jmol/?rev=8187&view=rev Author: hansonr Date: 2007-09-01 21:13:16 -0700 (Sat, 01 Sep 2007) Log Message: ----------- version=11.3.14 -- ready for release # bug fix: HDO not recognized as "water" # bug fix: rotateSelected MOLECULAR not around {0 0 0} # bug fix: -g ignored on -n option, even if -w is present # bug fix: unknown color palette could cause error # new feature: APPLICATION -q (quality) option # new feature: lcaoCartoon, mo, isosurface, pmesh: color [translucent [n]|opaque] [colors...] # adjustment: setting JPG default quality to 75, not 100 # new feature: {r,g,b} can be used in place of [r,g,b] for indicating color, # allowing programmatic color definition: # # r = 255; g = 255; b = 0; # background {@r,@g,@b} # new feature: expanded color command for properties # # color atoms property partialcharge "rwb" range -1.0 1.0 # # and reverse with range inverted: # # color atoms property partialcharge "rwb" range 1.0 -1.0 # new feature: unlimited user-defined color schemes: # # select none; # color "myname=[xff00ff] [xffff00] [xff00ff]" # # colors must be [xRRGGBB] format for this one # new feature: fully remappable isosurface using COLOR command: # # isosurface s1 molecular map mep # color $s1 "bwr" # color $s1 "rwb" range -0.2 0.2 # APPLICATION adjustment to console window scaling/size Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-02 04:07:39 UTC (rev 8186) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-02 04:13:16 UTC (rev 8187) @@ -1,8 +1,9 @@ -version=11.3.14_dev +version=11.3.14 # bug fix: HDO not recognized as "water" # bug fix: rotateSelected MOLECULAR not around {0 0 0} # bug fix: -g ignored on -n option, even if -w is present +# bug fix: unknown color palette could cause error # new feature: APPLICATION -q (quality) option # new feature: lcaoCartoon, mo, isosurface, pmesh: color [translucent [n]|opaque] [colors...] This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-09-02 04:23:14
|
Revision: 8189 http://jmol.svn.sourceforge.net/jmol/?rev=8189&view=rev Author: hansonr Date: 2007-09-01 21:23:09 -0700 (Sat, 01 Sep 2007) Log Message: ----------- 11.3.14 - last update - adds %l for labels (element number) Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-02 04:21:00 UTC (rev 8188) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-02 04:23:09 UTC (rev 8189) @@ -5,6 +5,8 @@ # bug fix: -g ignored on -n option, even if -w is present # bug fix: unknown color palette could cause error +# new feature: %l atomic element number + # new feature: APPLICATION -q (quality) option # new feature: lcaoCartoon, mo, isosurface, pmesh: color [translucent [n]|opaque] [colors...] This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2007-09-02 20:24:01
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Revision: 8196 http://jmol.svn.sourceforge.net/jmol/?rev=8196&view=rev Author: nicove Date: 2007-09-02 13:23:58 -0700 (Sun, 02 Sep 2007) Log Message: ----------- Version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-02 20:21:48 UTC (rev 8195) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-02 20:23:58 UTC (rev 8196) @@ -1,5 +1,9 @@ -version=11.3.14 +version=11.3.15_dev +# ----------------------------------------------------------------------------- + +#version=11.3.14 + # new feature: fully customizable popup menu -- see file jmol.mnu # # load menu jmol.mnu This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-09-03 17:13:33
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Revision: 8203 http://jmol.svn.sourceforge.net/jmol/?rev=8203&view=rev Author: hansonr Date: 2007-09-03 10:13:30 -0700 (Mon, 03 Sep 2007) Log Message: ----------- 11.3.15 version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-03 17:09:01 UTC (rev 8202) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-03 17:13:30 UTC (rev 8203) @@ -1,4 +1,4 @@ -version=11.3.15_dev +version=11.3.15 # new feature: fully customizable popup menu -- see file jmol.mnu # This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2007-09-03 18:06:55
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Revision: 8205 http://jmol.svn.sourceforge.net/jmol/?rev=8205&view=rev Author: nicove Date: 2007-09-03 11:06:51 -0700 (Mon, 03 Sep 2007) Log Message: ----------- Version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-03 17:50:00 UTC (rev 8204) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-03 18:06:51 UTC (rev 8205) @@ -1,5 +1,9 @@ -version=11.3.15 +version=11.3.16_dev +# ----------------------------------------------------------------------------- + +#version=11.3.15 + # new feature: fully customizable popup menu -- see file jmol.mnu # # load menu jmol.mnu This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-09-06 14:39:45
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Revision: 8208 http://jmol.svn.sourceforge.net/jmol/?rev=8208&view=rev Author: hansonr Date: 2007-09-06 07:39:37 -0700 (Thu, 06 Sep 2007) Log Message: ----------- version=11.3.16 # 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 # new feature: fully customizable popup menu -- see file jmol.mnu # # load menu jmol.mnu # # applet parameter param=menuFile value="jmol.mnu" # # application parameter -m filename # # mostly untested # # new feature: show menu # new feature: getProperty menu # # These deliver the current menu (as translated) in jmol.mnu format # ----------------------------------------------------------------------------- #version=11.3.14 # new feature: fully customizable popup menu -- see file jmol.mnu # # load menu jmol.mnu # # applet parameter param=menuFile value="jmol.mnu" # # largely untested # bug fix: HDO not recognized as "water" # bug fix: rotateSelected MOLECULAR not around {0 0 0} # bug fix: -g ignored on -n option, even if -w is present # bug fix: unknown color palette could cause error # new feature: %l atomic element number # new feature: APPLICATION -q (quality) option # new feature: lcaoCartoon, mo, isosurface, pmesh: color [translucent [n]|opaque] [colors...] # adjustment: setting JPG default quality to 75, not 100 # new feature: {r,g,b} can be used in place of [r,g,b] for indicating color, # allowing programmatic color definition: # # r = 255; g = 255; b = 0; # background {@r,@g,@b} # new feature: expanded color command for properties # # color atoms property partialcharge "rwb" range -1.0 1.0 # # and reverse with range inverted: # # color atoms property partialcharge "rwb" range 1.0 -1.0 # new feature: unlimited user-defined color schemes: # # select none; # color "myname=[xff00ff] [xffff00] [xff00ff]" # # colors must be [xRRGGBB] format for this one # new feature: fully remappable isosurface using COLOR command: # # isosurface s1 molecular map mep # color $s1 "bwr" # color $s1 "rwb" range -0.2 0.2 # APPLICATION adjustment to console window scaling/size # ----------------------------------------------------------------------------- #version=11.3.13 # this version introduces fully customizable color schemes # # new feature: .color for numbers and points delivers the # color associated with a given value in the current # coloring or propertyColorScheme. # (some number).color gives a color triple as a point {x y z} # {x y z}.color gives a hexadecimal string [xRRGGBB] # # # select atomno=3;color yellow # x = {atomno=3}.color # gives {255.0, 255.0, 0.0} # x = {atomno=3}.color.color # gives "[xFFFF00]" # # set propertyColorScheme "bwr" # x = {atomno=3}.partialcharge.color # # new feature: color ["schemeName"] RANGE [min] [max] # allows setting of color range and scheme so that color # values can be determined. This would be used for making # a color key using positionable ECHO text boxes: # # color "bwr" absolute -0.1 0.1 # x = (0.01).color # gives the point-color associated with that number # set echo myecho 100 100 # position # echo " " # just some space # color echo @x; background echo @x # color this bar the color of 0.01 # # new feature: show colorscheme "schemeName" # delivers "colorscheme = " followed by a string of color values. # without the scheme name, returns the current colorscheme listing # For example: show colorscheme "low" delivers: # # colorscheme = [xff0000] [xff2000] [xff4000] [xff6000] [xff8000] [xffa000] [xffc000] [xffe000] [xfff000] [xffff00] [xf0f000] # # setting an array variable to the color values: # # list = script("show colorscheme \"low\"")[15][0].split(" ") # # new feature: set userColorScheme [list of color names] # creates a colorscheme referred to as "user" and its reverse, "resu" # based on a list of color values: # # set userColorScheme red green [x00FFFF] blue # color atoms property partialcharge "user" range -1.0 1.0 # ----------------------------------------------------------------------------- #version=11.3.12 # bug fix: zoomTo 100% # bug fix: set language fr needs quotes but should not # bug fix: load multiple files inline causes null pointer exception # # new feature: APPLICATION: File|Export...|Export to Web Page # ----------------------------------------------------------------------------- #version=11.3.11 # bug fix: lcaoCartoon for sp center requires "sp2" not "sp" # bug fix: mo not showing titles # # new feature: lcaoCartoon rotate [x|y|z] degrees create "px" # new feature: adds Jaguar PLT plot file reader for isosurface # isosurface sign red blue "myfile.plt" # ----------------------------------------------------------------------------- #version=11.3.10 # bug fix: script window using swing thread start not from event queue # bug fix: state of multi-polymer protein cannot be restored # bug fix: dots nn% not operational # bug fix: molecular dipole and multiple frames # # new feature: molecular dipole for Gaussian files # # new feature: simple calculation of approximate dipole moment from charge distributions. # dipole molecular # from file value if provided # dipole calculate molecular # from "center of gravity" of charges calculation # # new feature: show frame # based on models in the current frame set, displays information about frames # # new feature: application option for web page export # # new feature: write JPG n "filename" # where n is the quality (<=100) # ----------------------------------------------------------------------------- #version=11.3.9 # bug fix for isosurface mapping of planes by MEP (see 11.3.2) # new feature: symmetryRange: load "someFile" {mmm nnn 1|0} range x.x where x.x is a maximum distance away from closest atom in the base cell # new feature: synchronization of applets using JavaScript # new feature: synchronization of applets using Jmol scripts: # # synchronize .|>|*|appletId[syncId] ON|OFF|SLAVE|command # # The synchronize (sync) command allows two or more applets to be synchronized in # terms of orientation. Move one with the mouse, and the other moves as well. # In addition, the sync command allows ANY command to be sent to one or more # other applets directly, without the intervention of JavaScript. # # Applets are identified by appletId (jmolApplet0, for instance) # along with an optional bracketed sync group identifier -- generally a random # number that identifies the page containing the controlling applet. If the # syncId is not given, then the ID for the page containing the controlling applet # is used. This feature is important for cross-frame synchronization only. # # # . this applet only # > all applets except this one # * all applets # appletId id of a specific applet # [syncId] (optional) a unique string of digits -- brackets included # # ON sync as driver (default) # OFF turn sync off # SLAVE turn sync on, but not as driver # command command to send # # for example: # # sync * # synchronize all applets as drivers # sync jmolApplet1 #syncs this applet with jmolApplet1 both as drivers # sync > "set echo top left;echo OK" # sends OK to top left of all OTHER applets # sync jmolApplet2[254678942] OFF # turns sync off for an applet ON A DIFFERENT PAGE # # or in a different FRAME # sync . OFF # turns sync off for this applet # # new Jmol.js feature: jmolGetSyncId(); jmolSetSyncId(id); # allows control over the sync ID via javascript. jmolSetSyncId(id) # should be called prior to jmolApplet() and should incorporate some sort of # random digits and no space characters. (A number is good.) # This should only be necessary for multi-frame pages. # ----------------------------------------------------------------------------- #version=11.3.8 # bug fix: isosurface color -- not operating for some isosurface types # bug fix: isosurface "xxxx.cube" -- not assigning proper default colors # bug fix: gamess reader MO fix # bug fix: state save of STRUCTURE misplaced # feature: adds adjustable scale for unitcell axes # ----------------------------------------------------------------------------- #version=11.3.7 # bug fix: reading of JVXL files for orbitals loses phase information # bug fix: ACD/Labs nonstandard cml "builtin" property reader # bug fix: isosurface interior cavity was not setting meshdata surfaceSet null # bug fix: select dna can select rna if chain is mixed hybrid dna+rna # ----------------------------------------------------------------------------- #version=11.3.6 # bug fix: inappropriate draw pick spinning for single point # bug fix: dots not available in multimodel mode # bug fix: multiple isosurface cavities incorrect in a multimodel environment # bug fix: isosurface cavity not filled completely # bug fix: nested ifs can cause last endif to throw error # bug fix: compiler bug working with very small real numbers # bug fix: Support for mol2 files with blank line after comments. # ----------------------------------------------------------------------------- #version=11.3.5 # bug fix: ACD/Labs nonstandard cml "builtin" property reader # note that xmlReader (SAX reader) is now set to ignore all DOCTYPE declarations # bug fix: odydata fix for files with \r\n for line ending # bug fix for PDB remediated T/DT difference of C5M/C7 # bug fix: set spin X was case-selective # bug fix: echo text not re-orienting on resize of applet or application # bug fix: multiple isosurface cavities in a multimodel environment # bug fix: missing set picking ident in popup window # bug fix: popup menu set picking label not working # ----------------------------------------------------------------------------- #version=11.3.4 # rough export of VRML using # # write VRML "myfile.wrl" # # includes colored balls and sticks; uncolored isosurfaces # ----------------------------------------------------------------------------- #version=11.3.3 # bug fix pmesh not working # bug fix for state after calculate surface, calculate hbonds, configuration, dynamic variable definition in multimodel environment (ModelSet::addStateScript) # NEW FEATURES from the 2007 Gordon Research Conference on Visualization in Science and Education: # # internal dataFrame concept # # new command: ramachandran # # new command: quaternion [w x y z] [derivative] # # TODO: frame menu # TODO: write VMRL # preliminary Maya export -- sets the stage for any number of export frameworks. # ----------------------------------------------------------------------------- #version=11.3.2 # bug fix: set picking label # bug fix: minus-sign "fix" in 11.3.1 broke all {x -y z} notation # bug fix: state for phased atomic orbitals does not preserve red/blue color # bug fix: mo opaque causing "invalid argument" when no MOs # bug fix: isosurface cavity molecular caused exception # feature: adds isosurface capability to map MO and MEP data onto planes # ----------------------------------------------------------------------------- #version=11.3.1 # bug fix: debugscript on;center 3-5; "-" missing # bug fix: zoomTo (5-7) read as "5 to -7" # bug fix: move with time < 0.03 seconds causes molecule to disappear # bug fix: hover interruption # bug fix: image offsets in creating JPG image if model has been moved by CTRL-ALT-LEFT drag # ----------------------------------------------------------------------------- #version=11.3.0 # perspectiveModel 11 default # bug fix for 3D text echo staying in window # bug fix for draw text+translucency # bug fix for draw text not hovering for points # bug fix for multiple draw objects in show state # bug fix for spin save reversed direction # bug fix for CdkAdapter not having auxiliaryInfo data # # adds the ability to find the coordinate of a specific # draw object vertex using $objName[vertexId] as in # draw p perp plane (atomno=1) (atomno=2) # x = $p[3] # draw pt1 $p[1] # ----------------------------------------------------------------------------- #version=11.1.49 # bug fix for Gaussian file reader fix for very large negative MO coefficients # bug fix for move not releasing isInMotion # bug fix for x = "testing"[0], x = "testing"[-1], "testing".split("t")[0], and "testing".split("t")[-1] # bug fix for select {*}[0], {*}[-1], etc., which now counts from the end back # adds proper indents on debugscript for if/else/endif # allows "jmolscript:" for embedded scripts and callbacks # ----------------------------------------------------------------------------- #version=11.1.48 # bug fix for gamess reader MO fix # bug fix for mopac GRAPHF file fix (resolver thought MOL) # bug fix for lcaocartoon "lp" fix for AX3E and AX2E # ----------------------------------------------------------------------------- #version=11.1.47 # bug fix for compound document reader not reading enough short segment pointers # bug fix for Spartan reader not recognizing 5D orbital problem # bug fix for animation skipping frames # ----------------------------------------------------------------------------- #version=11.1.46 # bug fix for Jvxl.jar standalone application not having complete set of class files (jvxl) # adds inline help support for Jmol application running under Java 6 (Java 1.6.xx) # bug fix for inappropriate pre-JVM12 menu items not disabled # ----------------------------------------------------------------------------- #version=11.1.45 # bug fix for animFrameCallback not indicating animation direction # bug fix for help not working and help URL not displaying (app) # bug fix for app not writing state from File...Export menu (app) # bug fix for retaining the last-saved file type selected for Image export (app) # bug fix for "wait" not recognizing if it is just a syntax check (app) # ----------------------------------------------------------------------------- #version=11.1.44 # bug fix for inability to specify fractional coordinates: adds fx, fy, fz as # select fx < 0.5 and fy < 0.5 and fz < 0.5 # aveFracX = {molecule=1}.fx # bug fix for inability to use x,y,z,fx,fy,fz with cartesian points # bug fix for select BONDS ({...}) not preserved in state # bug fix for geosurface not always restored from saved state # bug fix for strandcount saved explicitly forces bioshape load # ----------------------------------------------------------------------------- #version=11.1.43 # bug fix for labels mysteriously disappearing. Also probably taking up HUGE amounts of hashtable space. # bug fix for hydrogen bond calculation with incomplete nucleic acid definitions. # bug fix for "set picking draw" crashing Jmol # bug fix for strandCount not carrying over to meshRibbon # bug fix for geosurface/dots save/restore state exception # bug fix for save state using "measurements off" instead of "set measurements off" # ----------------------------------------------------------------------------- #version=11.1.42 # bug fix for lack of updating of certain variable predefined expressions # bug fix for smiles nonfunctional # bug fix for load append and structure commands # bug fix for load files losing structure and cartoons # bug fix for multiple frames displayed does not show Select...Elements menu # bug fix for select @x not functioning where x = {atom expression} or x = "atom expression" # bug fix for {atom expression}.ident nonfunctional # code refactoring Frame --> ModelSet and ModelLoader # code refactoring modelframe --> modelset package # code refactoring shapebio --> shapebio + molsetbio packages # code refactoring dissociates Mps.MpsShape from Mps as BioShape # code refactoring removes Mps.Mpsmodel # code refactoring Mps --> BioShapeCollection # code refactoring greatly simplifies BioShapeCollection subclasses # ----------------------------------------------------------------------------- #version=11.1.41 # bug fix for load with explicit spacegroup not respecting normalization choice # bug fix for symop=nijk selecting base atoms when not appropriate # bug fix for select specialposition non-functional # bug fix for adding atoms but mads[] going stale # slight redefinition of "special position" # bug fix for structure loss on load append. (structure is supposed to be recalculated). # adds language switching for Open / Save dialog boxes and full menuing system in Jmol application # adds "structure" command -- structure [helix|sheet|turn|none] (atom expression) # adds "save/restore structure" command # ----------------------------------------------------------------------------- #version=11.1.40 # bug fix for backgroundModel and save state # bug fix for load append with spacegroups causing atoms to be repositioned # bug fix for anim playrev in loop mode causing animation to stall # ----------------------------------------------------------------------------- #version=11.1.39 # several bug fixes: # # bug fix for mo data misreading in smol files # bug fix for lcaoCartoon "s" giving incomplete spheres # bug fix for select symop=3555 not giving proper atoms when load "" {444 666 0} # bug fix for PDB files not supplying information about residues for the popup menu. # bug fix in frame range 1.0 when file 1 has only one model. # ----------------------------------------------------------------------------- #version=11.1.38 # bug fix for opaque triangles missing one pixel on right side when translucent objects are present. # bug fix for label alignments sometimes not being saved properly in the state # bug fix for animFrameCallback giving multiple callbacks -- still there, but identified now # in terms of whether animation is on or not in the 7th parameter being 1 or 0: # # function animFrameCallback(app,frame,fileno,modelno,firstno,lastno,isRunning){...} # ----------------------------------------------------------------------------- #version=11.1.37 # fixes bugs in draw and unicode label state definitions # adds simplistic <sub></sub> <sup></sup> to text, including echo, label, hover, etc. # fixes popup menu to better deal with multiple file context # update of Turkish translation # ----------------------------------------------------------------------------- #version=11.1.36 # build: renames applet files JmolApplet0*.jar and JmolAppletSigned0*.jar # # bug fixes for isosurface in multi-file environment # # bug fix and additional work in relation to translations # # zoomTo (atom expression) 0 # # with options # # zoomTo (atom expression) 0+n # zoomTo (atom expression) 0-n # zoomTo (atom expression) 0*n # zoomTo (atom expression) 0/n # # also # # moveTo timeSec {x y z w} (atom expression) [zoom factor] # and # moveTo timeSec {x y z w} 0 transX transY (atom expression) [zoom factor] # # where [zoom factor] is x, where x > 0 # or # [0] [[+ | - | * | /] x] # # # app fix for Edit...preferences not properly refreshing for axes and boundbox # ----------------------------------------------------------------------------- #version=11.1.35 # fix for x = {...}.resno and {...}.groupID # fix for select resno=-1 # first version of pt_BR translation # ----------------------------------------------------------------------------- #version=11.1.34 # language submenu # ----------------------------------------------------------------------------- #version=11.1.33 # bug fixes -- draw state, menu not updating, language submenu # ----------------------------------------------------------------------------- #version=11.1.32 # adds capability to define a property for selected atoms: # # select xxx # property_x = n.m # ----------------------------------------------------------------------------- #version=11.1.31 # adds capability to read data from selected fields (white-space delimited columns) in a file # # propertyDataField = 0 # no fields -- just read tokens # propertyDataField = 2 # data are in field 2 (second from the left) # propertyMatchField = 1 # data must match atomNo in field 1 and will be in # the field specified by propertyDataField # ----------------------------------------------------------------------------- #version=11.1.30 # full support for switching languages, including a new "language" menu item # # Jmol.js: # # jmolSetCallback("language", "de") # # Jmol scripting: # # language = "de" # # Menu: # # new language submenu with checkboxes. # # allows for efficient specific file reader options for the applet (particularly) # # adds _spinning variable # # adds LOAD xxx::myfile xxx indicating file type xyz, mol, etc. # # not important generally. # # adds PQR reader option, at least for PDB2PQR generated output # # better spin control during zoomTo and moveTo # spinning now detects that a zoomTo or moveTo operation is occurring # or the user is manipulating the model with the mouse, and pauses 1 second # for that operation to complete before resuming spinning # # hover now is turned off during spinning or user manipulation of the model # # zoomTo and moveTo the same location changed to no time delay # ----------------------------------------------------------------------------- #version=11.1.29 # code: totally reorganized isosurface code; new org/jmol/jvxl packages # # adds (1) isosurface functionxy "file:data.dat" ... # adds (2) isosurface functionxy "functionName" {x0 y0 z0} {-ni ...} ... # adds (3) isosurface functionxy "functionName" {x0 y0 z0} {-ni ...}{-nj ...} ... # # (1) "file:" allows reading of xy data from files for graphing f(x,y) # (2) ni<0 indicates JavaScript functionName will return a single string that # should be parsed for numeric data. # (3) ni<0, nj<0 indicates that JavaScript will fill the fourth parameter # of the function with an array of f[nX][nY] data values: # # Jmol: # # isosurface s1 functionXY "xyData" {-2 -2 -2} {21 0.1 0 0} {21 0 0.1 0} {21 0 0 0.1} # # JavaScript: (slow) # # function xyData(app, x, y) { # return func(x, y) # } # # Jmol: # # isosurface s2 functionXY "xyDataAsString" {-2 -2 -2} {-21 0.1 0 0} {21 0 0.1 0} {21 0 0 0.1} # # JavaScript: (much faster) # # function xyDataAsString(app, nX, nY) { # var s # for (var i = 0; i < nX; i++) # for (var j = 0; j < nY; j++) # s += "x_"+i+"\ty_"+j+"\t"+func(i,j)+"\n" # # //non-numeric formatting allowed but not necessary # # return s # } # # Jmol: # # isosurface s3 functionXY "xyDataAsArray" {-2 -2 -2} {-21 0.1 0 0} {-21 0 0.1 0} {21 0 0 0.1} # # JavaScript: (very fast) # # function xyDataAsArray(app, nX, nY, fxy) { # for (var i = 0; i < nX; i++) # for (var j = 0; j < nY; j++) # fxy[i][j] = func(i,j) # } # # (2) and (3) are very fast; (1) is the original method, but it is slow. # # MAYSCRIPT expanded # # for the Wiki or any application where absolutely no JavaScript # is to be allowed, simply remove the MAYSCRIPT parameter, which # now covers all aspects of JavaScript interaction from within Jmol # # # adds applySymmetryToBonds (default: FALSE) # # applySymmetryToBonds # # When set TRUE, this flag instructs Jmol when applying symmetry # to atoms, as in "load xxx.cif {1 1 1}", to also apply symmetry # to the bonds indicated in the file. The flag is useful when # normal Jmol autobonding would not properly connect atoms, but # the model is "molecular" -- the base atom coordinates are correct # for whole molecules. The flag should NOT be used in cases where # the application of symmetry operations creates new bonds that # were not present in the original set, as for quartz.cif, where # there is only one bond initially, and after applying symmetry # new bonds are created that are between atoms that were created # using two different symmetry operations. # # adds isosurface HOMO/LUMO [+/- n] # # better isosurface plane rendering, especially in regard to meshes # bug fix in isosurface contour -n going WAY back to before 10.9.60 # refactoring of all isosurface-related classes # support for Spartan MO HOMO # # adds isosurface POCKET [cavity] sasurface # adds isosurface INTERIOR [cavity] sasurface # # adds load TRAJECTORY -- for a single file with multiple models all with # the same number of atoms. Atom locations can also be updated on the # fly using the data statement. # # adds TRAJECTORY n command -- like FRAME or MODEL, but never more # than one model at a time displayed, because there is only one set # of atoms. # # adds script: option for callbacks set from within Jmol. That is, callbacks # can either be to host page JavaScript functions or to Jmol scripts. This # will allow interactive sessions without external JavaScript. # # set pickcallback "script: script doCallback.spt" # # adds resizeCallback because certain positioning of echos and sizing of the # structure may require method intervention after the resizing # # adds translucency for echo and hover, both text and backgrounds # # adds echo script to defined state # # adds hourglass cursor during MO/Isosurface operations # # fixes inoperative "set pickingstyle measures on" # ----------------------------------------------------------------------------- #version=11.1.28 # adds # # a = script("some script command") # a = javascript("some javascript") # # putting output into a from commands such as "show" or "getProperty", for instance. # # reinstates tempManager properly. # # adds support for CAChe CSF files with MOPAC (AM1, PM3, etc.), # Density Functional, and Extended Huckel Gaussian/Slater-based molecular orbitals. # # CHANGES DEFAULT RENDERING FOR MOLECULAR ORBITALS TO: MESH NOFILL FRONTONLY # # adds MOPAC 2007 graphf output reader (gpt2 files, MOPAC molecular orbitals) # based on the VERY latest version (not released yet), which includes # "MOPAC-Graphical data" on the first line, character index 6. # # adds # # mo HOMO [+/- n] # mo LUMO [+/- n] # # fixes bugs found by FindBugs: # # labels: default z setting for labels (set labelFront, set labelGroup, set labelAtom) # was not being recorded properly # move: with slab or zoom was doing integer math # GhemicalMMReader -- was incorrectly assigning aromatic to bond type 4 via fall-through of switch # # adds xodydata reading of "boundary" as unitcell # enhances default axis rendering for axes unitcell # # adds expanded isosurface-related commands: # # draw list # isosurface list # lcaocartoon list # (mo list) -- not particularly useful # pmesh list # # Listing gives id, number of vertices, number of polygons, visibility, # and title (usually the command that was given that created this isosurface) # # CHANGED BEHAVIOR FOR ISOSURFACE COMMAND WITHOUT ID INDICATED: # # Now if no ID is indicated, the previous ID is used for all commands # EXCEPT "isosurface delete", which deletes all isosurfaces. # # This is a change from Jmol 10.2 and 11.0, where if you leave # off the ID, a new isosurface is created. # # This was a needed change to prevent unwanted multiple isosurfaces. # # CHANGED BEHAVIOR FOR ISOSURFACE DEFAULT COLOR # # The default isosurface color no longer changes shade among 5 possible shades. # That was necessary only because it was easy to mistakenly make multiple # isosurfaces that otherwise would look the same. # ----------------------------------------------------------------------------- #version=11.1.27 # fixes two state bugs: # 1) dots/geosurface not being saved properly in state # 2) animation parameters not being saved properly in state # ----------------------------------------------------------------------------- #version=11.1.26 # fixes two nasty bugs relating to isosurfaces and JVXL files. # -- JVXL files created from molecular orbitals will show up with no color # in 11.1.0 - 11.1.25 because of a missing number in the definition line :( # -- JVXL files created from molecular orbitals will show unwanted cross-over # surfaces from + to -. # ----------------------------------------------------------------------------- #version=11.1.25 # --fully dissociates geosurface from dots; # --allows coloring and transparency of geosurface # similarly to the way stars are colored # ----------------------------------------------------------------------------- #version=11.1.24 # refactored Geodesic3D, Dots, DotsRenderer # independent dots/geosurface # # isosurface CAVITY # ----------------------------------------------------------------------------- #version=11.1.23 # fixes a number of bugs, some critical # # adds isosurface CAVITY x.xx -- a new way to depict the cavities of # a molecule in terms of color. # ----------------------------------------------------------------------------- #version=11.1.21/22 # adds # # load file "=xxxx" and set loadFormat "http://....../%FILE..... # load files ..... # just a cleaner version of loading multiple files. # load append ..... # APPENDS the file(s) or model(s) as new frames onto the current set. # data append ..... # same thing, but inline # # isosurface MODEL n # pmesh MODEL n # isosurface within x.x (what) # # Introduces "real" color translucency # # color xxxx translucent N # # where N is -1 to 9. # # OR OR # translucent -1 same as Jmol 10.2 # translucent 0.0 opaque # through # translucent 1.0 transparent (invisible) # # translucent 2 0.125 32 1/8 translucency (slightly translucent) # translucent 3 0.25 64 2/8 translucency # translucent 4 0.375 96 3/8 translucency # translucent 5 0.5 128 4/8 translucency (default) # translucent 6 0.625 160 5/8 translucency # translucent 7 0.75 192 6/8 translucency # translucent 8 0.825 224 7/8 translucency (very sheer) # translucent 9 1.00 255 8/8 transparent (invisible) # ----------------------------------------------------------------------------- #version=11.1.20 # cleans up axes/boundbox/unitcell business # # allows for individually colored axes: # # color axis1 ... # color axis2 ... # color axis3 ... # color axes ... (of course) # # and these objects are considered more like background -- # colors and sizes persist past file load # # to turn on and off without messing with size, just use # # showAxes = true # showBoundBox = true # # etc. # ----------------------------------------------------------------------------- #version=11.1.19 # allows comparison of user-defined atom properties in SELECT: # # select property_myprop < 1e-5; # # and # # x = {carbon}[5].property_test # x = {carbon}.property_test.min # x = {carbon}.property_test.max # # etc. # # This is it! :) # ----------------------------------------------------------------------------- #version=11.1.18 # introduces user-definable atom properties that can be used # to color isosurfaces: # # x = load("file.dat"); # isosurface variable x # simple 100% vdw radius mapping # # select 1.3 # data "property_myprop @x" # isosurface property_myprop # # allows isosurface mapping of general atom properties: # # isosurface sasurface colorscheme bwr map property temperature # # adds "bwr" colorscheme as opposed to "rwb", which I think is backward. # # isosurface -- now supports APBS ( ) # molecular electrostatic potential output files # # write -- modified to allow unquoted filename in # write isosurface file.name # # jvxl 1.0 -- adds ANGSTROMS flag on line with # of atoms (line 3) # ----------------------------------------------------------------------------- #version=11.1.17 # deprecation of SET # ------------------ # # The "SET" command is no longer necessary. Anything that could have # been set using "SET x .... " can now be set using # # x = .... # # This allows for a much cleaner interface because we simply make # settings in a normal sort of way: # # axes on # axes = molecular # # measures = angstroms # # It will take a bit more to make it all consistent, but the idea # is that there are then some special reserved variables that # mean something special when set, like "bondmode" # # This build allows for the applet to be "bare-bones" -- only the # essential classes included in the Jar file; others never included # or possibly in accompanying jar files, such as, perhaps, JmolPopupMenu.jar, # JmolNavigation.jar, JmolBio.jar, Jm olSurface.jar, JmolXtal.jar, etc. # # Then a developer can slim down the download. 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 # ----------------------------------------------------------------------------- #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 ...})" # # set x = {oxygen}.xyz # set y = {carbon}.xyz # draw @x # draw @y # draw line1 @x @y # # and # # set x = {carbon}[3][5] # select @x_set # color green # # set x = {carbon or oxygen}.bonds # select BONDS @x_set # 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= Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-06 14:36:52 UTC (rev 8207) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-06 14:39:37 UTC (rev 8208) @@ -1,4 +1,4 @@ -version=11.3.16_dev +version=11.3.16 # new feature: byElement and byResidue color schemes allow # customized element and residue coloring schemes. @@ -13,6 +13,10 @@ # 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. @@ -32,9 +36,13 @@ # # so this opens the door to user-created residue coloring schemes. # -# color "byResidu_Mine=[x......] [x......]..." +# color "byResidue_Mine=[x......] [x......]..." # nogroup ALA ... # +# then +# +# color cartoons "byResidue_Mine" + # ----------------------------------------------------------------------------- #version=11.3.15 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-09-06 14:50:36
|
Revision: 8209 http://jmol.svn.sourceforge.net/jmol/?rev=8209&view=rev Author: hansonr Date: 2007-09-06 07:50:17 -0700 (Thu, 06 Sep 2007) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-06 14:39:37 UTC (rev 8208) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-06 14:50:17 UTC (rev 8209) @@ -31,7 +31,7 @@ # 11 LEU, LYS, MET, PHE, PRO, # 16 SER, THR, TRP, TYR, VAL, # 21 ASX, GLX, UNK, -# 24 A, +A, G, +G, I, +I +# 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. This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2007-09-07 05:04:46
|
Revision: 8212 http://jmol.svn.sourceforge.net/jmol/?rev=8212&view=rev Author: nicove Date: 2007-09-06 22:04:33 -0700 (Thu, 06 Sep 2007) Log Message: ----------- Version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-07 01:12:32 UTC (rev 8211) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-07 05:04:33 UTC (rev 8212) @@ -1,5 +1,9 @@ -version=11.3.16 +version=11.3.17_dev +# ----------------------------------------------------------------------------- + +#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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2007-09-09 20:29:41
|
Revision: 8228 http://jmol.svn.sourceforge.net/jmol/?rev=8228&view=rev Author: nicove Date: 2007-09-09 13:29:14 -0700 (Sun, 09 Sep 2007) Log Message: ----------- Version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-09 20:04:21 UTC (rev 8227) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-09 20:29:14 UTC (rev 8228) @@ -1,5 +1,9 @@ -version=11.3.17 +version=11.3.18_dev +# ----------------------------------------------------------------------------- + +#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 @@ -95,7 +99,6 @@ # new feature: someArray.sub("string") adds string to left of each item # colorManager clean-up - # ----------------------------------------------------------------------------- This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2007-09-10 04:32:59
|
Revision: 8233 http://jmol.svn.sourceforge.net/jmol/?rev=8233&view=rev Author: nicove Date: 2007-09-09 21:32:58 -0700 (Sun, 09 Sep 2007) Log Message: ----------- Version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-10 04:26:28 UTC (rev 8232) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-10 04:32:58 UTC (rev 8233) @@ -1,5 +1,9 @@ -version=11.3.18 +version=11.3.19_dev +# ----------------------------------------------------------------------------- + +#version=11.3.18 + # critical bug fix for 11.3.17 in regard to serialization of arrays # also introduces # This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-09-11 04:44:04
|
Revision: 8241 http://jmol.svn.sourceforge.net/jmol/?rev=8241&view=rev Author: hansonr Date: 2007-09-10 21:44:01 -0700 (Mon, 10 Sep 2007) Log Message: ----------- 11.3.19 version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-11 04:39:48 UTC (rev 8240) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-11 04:44:01 UTC (rev 8241) @@ -1,5 +1,6 @@ -version=11.3.19_dev +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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2007-09-11 06:30:38
|
Revision: 8245 http://jmol.svn.sourceforge.net/jmol/?rev=8245&view=rev Author: nicove Date: 2007-09-10 23:30:32 -0700 (Mon, 10 Sep 2007) Log Message: ----------- Version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-11 06:23:49 UTC (rev 8244) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-11 06:30:32 UTC (rev 8245) @@ -1,5 +1,9 @@ -version=11.3.19 +version=11.3.20_dev +# ----------------------------------------------------------------------------- + +#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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2007-09-11 16:59:57
|
Revision: 8251 http://jmol.svn.sourceforge.net/jmol/?rev=8251&view=rev Author: nicove Date: 2007-09-11 09:59:55 -0700 (Tue, 11 Sep 2007) Log Message: ----------- Version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-11 12:40:52 UTC (rev 8250) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-11 16:59:55 UTC (rev 8251) @@ -1,5 +1,9 @@ -version=11.3.20 +version=11.3.21_dev +# ----------------------------------------------------------------------------- + +#version=11.3.20 + # bug fix for arrows way too fat (introduced in 11.3.19) :( # ----------------------------------------------------------------------------- This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-09-13 10:54:09
|
Revision: 8260 http://jmol.svn.sourceforge.net/jmol/?rev=8260&view=rev Author: hansonr Date: 2007-09-13 03:54:08 -0700 (Thu, 13 Sep 2007) Log Message: ----------- 11.3.21 version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-13 10:51:02 UTC (rev 8259) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-13 10:54:08 UTC (rev 8260) @@ -1,4 +1,4 @@ -version=11.3.21_dev +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. This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2007-09-13 21:03:30
|
Revision: 8264 http://jmol.svn.sourceforge.net/jmol/?rev=8264&view=rev Author: nicove Date: 2007-09-13 14:03:23 -0700 (Thu, 13 Sep 2007) Log Message: ----------- Version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-13 20:55:12 UTC (rev 8263) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-13 21:03:23 UTC (rev 8264) @@ -1,4 +1,9 @@ -version=11.3.21 +version=11.3.22_dev + +# ----------------------------------------------------------------------------- + +#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. This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-09-15 05:59:34
|
Revision: 8273 http://jmol.svn.sourceforge.net/jmol/?rev=8273&view=rev Author: hansonr Date: 2007-09-14 22:59:32 -0700 (Fri, 14 Sep 2007) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-15 05:43:17 UTC (rev 8272) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-15 05:59:32 UTC (rev 8273) @@ -22,7 +22,7 @@ # var dist = {atomno=i}.distance({atomno=j}) # # if (dist < 1.77) -# print "i-j: " + i + "," + j + " " + dis%2 +# print "i-j: " + i + "," + j + " " + dist%2 # measure {atomno=i} {atomno=j} # endif # This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-09-15 06:01:17
|
Revision: 8274 http://jmol.svn.sourceforge.net/jmol/?rev=8274&view=rev Author: hansonr Date: 2007-09-14 23:01:16 -0700 (Fri, 14 Sep 2007) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-15 05:59:32 UTC (rev 8273) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-15 06:01:16 UTC (rev 8274) @@ -15,6 +15,12 @@ # 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) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-09-15 14:54:59
|
Revision: 8276 http://jmol.svn.sourceforge.net/jmol/?rev=8276&view=rev Author: hansonr Date: 2007-09-15 07:54:57 -0700 (Sat, 15 Sep 2007) Log Message: ----------- version=11.3.23 VERSION Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-15 14:38:37 UTC (rev 8275) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-09-15 14:54:57 UTC (rev 8276) @@ -1,6 +1,6 @@ version=11.3.23 -# preliminary full script flow control support: +# VERSION full script flow control support: # if / else if / else / end if # for / end for This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |