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
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