From: <ha...@us...> - 2013-06-27 08:03:02
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Revision: 18368 http://sourceforge.net/p/jmol/code/18368 Author: hansonr Date: 2013-06-27 08:02:58 +0000 (Thu, 27 Jun 2013) Log Message: ----------- ___JmolVersion="13.1.18" JmolVersion="13.1.17_dev_2013.06.27" TODO: PyMOL uniqueAtomSettings for transparency -- will require by-vertex translucent option new feature: CASTEP reader filter option q=all new feature: set picking DRAGLIGAND -- won't move the protein new feature: isosurface SLAB TRANSLUCENT 0.x color -- inherits color of isosurface when color parameter is absent -- TODO - properly save in JVXL file new feature: CIF reader upgrade to allow multicharacter chain specs. -- See 1bgl_1bgm.cif -- automatically switches to chainCaseSensitive if multi-character or lower-case chains are read in a CIF file. -- note that in certain cases quotation marks will be needed: select chain=0123 NOT OK select :0123 NOT OK select chain="0123" OK select :"0123" OK select :"A*" or :"A'" or :'A"' or :"A\"" new feature: {atomset1}.distance.min({atomset2}) -- returns an array -- minimum distance of each atom in atomset1 to any atom in atomset2 new feature: {atomset1}.distance.max({atomset2}) -- returns an array -- maximum distance of each atom in atomset1 to any atom in atomset2 new feature: compare({atomset1} {atomset2} "ccCCN" "bonds") new feature: {1.1}.find("ccCCN", "BONDS") new feature: set translucent -- default TRUE : translucent objects are fully translucent -- FALSE: translucent objects are opaque to other translucent objects bug fix: CrystalReader broken by recent change to simpleReplace() bug fix: PyMOL movie start frame bug fix: PyMOL putty broken bug fix: pdbAddHydrogens may miss O3' or O5' H atoms at end of DNA strands bug fix: pdbAddHydrogens may miss H in first group of a chain bug fix: set defaultDrawArrowScale broken bug fix: "ligand" should include all _g=0 (nonPDB atoms) bug fix: applet getpropertyAsArray("bondInfo") fails bug fix: JSmol script/scriptWait nuance with moveto. -- when using scriptWait with HTML5, there can be no threading bug fix: invertSelected on trajectory causes nullPointerException bug fix: POLYHEDRA with faceCenterOffset not saved in state properly; EDGES option nonfunctional bug fix: JavaScript not returning arrays properly from Jmol.getPropertyXXXX() -- very important to have {} after j2sNative directive! bug fix: COMPARE could rotate to less-good fit with SMARTS search bug fix: draw ARROW ATOM/BOND broken bug fix: animation MORPH broken for non-PyMOL files -- load trajectory ({0 6}) 1cdr.pdb -- animation MORPH 10 -- animation ON -- load trajectory "test1.pdb" "test2.pdb" -- animation MORPH 30 -- animation ON bug fix: draw ARROW ATOM/BOND broken bug fix: draw ARROW with offset disallows set picking draw adjustments bug fix: concurrrent loading of two cif files by two different applets fails bug fix: draw LINEDATA not operative (undocumented, for state; from draw xxx INTERSECT yyy) -- needs revision to create DATA option; can be huge and very long to process state file bug fix: load :2-butanone fails bug fix: PyMOL volume map data saved from PyMOL 1.6 has slightly different data structure bug fix: jvxl reader ignores jvxlVertexColorData bug fix: ellipsoid rendering problems code: MagRes/CASTEP reader upgrades code: color/translucent/opaque clean up in ScriptEvaluator 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 2013-06-27 07:59:47 UTC (rev 18367) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-27 08:02:58 UTC (rev 18368) @@ -13,31 +13,15 @@ JmolVersion="13.1.17_dev_2013.06.27" -new feature: CASTEP reader filter option q=all -bug fix: CrystalReader broken by recent change to simpleReplace() -code: MagRes/CASTEP reader upgrades -bug fix: PyMOL movie start frame -bug fix: PyMOL putty broken -bug fix: pdbAddHydrogens may miss O3' or O5' H atoms at end of DNA strands -bug fix: pdbAddHydrogens may miss H in first group of a chain -bug fix: set defaultDrawArrowScale broken - TODO: PyMOL uniqueAtomSettings for transparency -- will require by-vertex translucent option +new feature: CASTEP reader filter option q=all new feature: set picking DRAGLIGAND -- won't move the protein - -bug fix: "ligand" should include all _g=0 (nonPDB atoms) - new feature: isosurface SLAB TRANSLUCENT 0.x color -- inherits color of isosurface when color parameter is absent -- TODO - properly save in JVXL file - -bug fix: applet getpropertyAsArray("bondInfo") fails -bug fix: JSmol script/scriptWait nuance with moveto. - -- when using scriptWait with HTML5, there can be no threading - new feature: CIF reader upgrade to allow multicharacter chain specs. -- See 1bgl_1bgm.cif -- automatically switches to chainCaseSensitive if multi-character @@ -48,48 +32,53 @@ select chain="0123" OK select :"0123" OK select :"A*" or :"A'" or :'A"' or :"A\"" - -bug fix: invertSelected on trajectory causes nullPointerException -bug fix: POLYHEDRA with faceCenterOffset not saved in state properly; EDGES option nonfunctional - new feature: {atomset1}.distance.min({atomset2}) -- returns an array -- minimum distance of each atom in atomset1 to any atom in atomset2 new feature: {atomset1}.distance.max({atomset2}) -- returns an array -- maximum distance of each atom in atomset1 to any atom in atomset2 +new feature: compare({atomset1} {atomset2} "ccCCN" "bonds") +new feature: {1.1}.find("ccCCN", "BONDS") +new feature: set translucent + -- default TRUE : translucent objects are fully translucent + -- FALSE: translucent objects are opaque to other translucent objects +bug fix: CrystalReader broken by recent change to simpleReplace() +bug fix: PyMOL movie start frame +bug fix: PyMOL putty broken +bug fix: pdbAddHydrogens may miss O3' or O5' H atoms at end of DNA strands +bug fix: pdbAddHydrogens may miss H in first group of a chain +bug fix: set defaultDrawArrowScale broken +bug fix: "ligand" should include all _g=0 (nonPDB atoms) +bug fix: applet getpropertyAsArray("bondInfo") fails +bug fix: JSmol script/scriptWait nuance with moveto. + -- when using scriptWait with HTML5, there can be no threading +bug fix: invertSelected on trajectory causes nullPointerException +bug fix: POLYHEDRA with faceCenterOffset not saved in state properly; EDGES option nonfunctional bug fix: JavaScript not returning arrays properly from Jmol.getPropertyXXXX() -- very important to have {} after j2sNative directive! bug fix: COMPARE could rotate to less-good fit with SMARTS search bug fix: draw ARROW ATOM/BOND broken - -new feature: compare({atomset1} {atomset2} "ccCCN" "bonds") -new feature: {1.1}.find("ccCCN", "BONDS") - bug fix: animation MORPH broken for non-PyMOL files -- load trajectory ({0 6}) 1cdr.pdb -- animation MORPH 10 -- animation ON -- load trajectory "test1.pdb" "test2.pdb" -- animation MORPH 30 - -- animation ON - + -- animation ON bug fix: draw ARROW ATOM/BOND broken bug fix: draw ARROW with offset disallows set picking draw adjustments bug fix: concurrrent loading of two cif files by two different applets fails bug fix: draw LINEDATA not operative (undocumented, for state; from draw xxx INTERSECT yyy) -- needs revision to create DATA option; can be huge and very long to process state file - -code: color/translucent/opaque clean up in ScriptEvaluator bug fix: load :2-butanone fails bug fix: PyMOL volume map data saved from PyMOL 1.6 has slightly different data structure bug fix: jvxl reader ignores jvxlVertexColorData bug fix: ellipsoid rendering problems -new feature: set translucent - -- default TRUE : translucent objects are fully translucent - -- FALSE: translucent objects are opaque to other translucent objects +code: MagRes/CASTEP reader upgrades +code: color/translucent/opaque clean up in ScriptEvaluator ============================================================================= This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |