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From: <ha...@us...> - 2008-07-17 05:11:07
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Revision: 9606
http://jmol.svn.sourceforge.net/jmol/?rev=9606&view=rev
Author: hansonr
Date: 2008-07-17 05:11:05 +0000 (Thu, 17 Jul 2008)
Log Message:
-----------
new Quaternion algorithm uses double precision
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 2008-07-17 05:10:21 UTC (rev 9605)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-17 05:11:05 UTC (rev 9606)
@@ -3,10 +3,10 @@
version=11.5.48_dev
+# code: simpler matrix-->quaternion code
# bug fix: 11.5.47 shows oddly sized arrow for very first rendering
# bug fix: quaternion frame "n" after rotationSelected does not reset NH hydrogen positions
# new feature: // at beginning of a line marks comments
-
# -----------------------------------------------------------------------------
#version=11.5.47
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From: <ha...@us...> - 2008-07-19 14:09:35
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Revision: 9617
http://jmol.svn.sourceforge.net/jmol/?rev=9617&view=rev
Author: hansonr
Date: 2008-07-19 14:09:23 +0000 (Sat, 19 Jul 2008)
Log Message:
-----------
11.5.48 VERSION
# new feature: mol file bond type 8 as partial
# code: compiler error reporting improved
# bug fix: PDB site definition does not ignore empty site definitions
# bug fix: DEFINE can cause compiling error, e.g. "[2MO]" in 1tmo
# bug fix: quaternion derivative DRAW arrows placed on residue i+1 instead of residue i
# bug fix: connect aromatic auto; select connected([bond type],...)
# bug fix: queue thread termination when applets are off screen
# bug fix : sheetsmoothing not consistent among structures in multi-chain systems
# bug fix: messages not sent to messageCallback
# code: simpler matrix-->quaternion code
# bug fix: 11.5.47 shows oddly sized arrow for very first rendering
# bug fix: quaternion frame "n" after rotationSelected does not reset NH hydrogen positions
# new feature: // at beginning of a line marks comments
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 2008-07-19 14:04:07 UTC (rev 9616)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-19 14:09:23 UTC (rev 9617)
@@ -1,7 +1,7 @@
# Developers: to add a description of changes you have made,
# add it on line starting with # below the "version=..." line
-version=11.5.48_dev
+version=11.5.48
# new feature: mol file bond type 8 as partial
# code: compiler error reporting improved
@@ -16,6 +16,7 @@
# bug fix: 11.5.47 shows oddly sized arrow for very first rendering
# bug fix: quaternion frame "n" after rotationSelected does not reset NH hydrogen positions
# new feature: // at beginning of a line marks comments
+
# -----------------------------------------------------------------------------
#version=11.5.47
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From: <ni...@us...> - 2008-07-19 14:50:09
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Revision: 9618
http://jmol.svn.sourceforge.net/jmol/?rev=9618&view=rev
Author: nicove
Date: 2008-07-19 14:49:33 +0000 (Sat, 19 Jul 2008)
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 2008-07-19 14:09:23 UTC (rev 9617)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-19 14:49:33 UTC (rev 9618)
@@ -1,8 +1,12 @@
# Developers: to add a description of changes you have made,
# add it on line starting with # below the "version=..." line
-version=11.5.48
+version=11.5.49_dev
+# -----------------------------------------------------------------------------
+
+#version=11.5.48
+
# new feature: mol file bond type 8 as partial
# code: compiler error reporting improved
# bug fix: PDB site definition does not ignore empty site definitions
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From: <ni...@us...> - 2008-07-21 17:20:51
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Revision: 9624
http://jmol.svn.sourceforge.net/jmol/?rev=9624&view=rev
Author: nicove
Date: 2008-07-21 17:20:47 +0000 (Mon, 21 Jul 2008)
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 2008-07-21 15:12:30 UTC (rev 9623)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-21 17:20:47 UTC (rev 9624)
@@ -1,8 +1,12 @@
# Developers: to add a description of changes you have made,
# add it on line starting with # below the "version=..." line
-version=11.5.49
+version=11.5.50_dev
+# -----------------------------------------------------------------------------
+
+#version=11.5.49
+
# bug fix: strange "scripted: ?" message with measurements removed
# bug fix: extra values in measure reporting, and wrong format
# bug fix: 11.5.48 is broken for scripts with array definitions such as
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From: <ha...@us...> - 2008-10-26 23:26:31
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Revision: 10152
http://jmol.svn.sourceforge.net/jmol/?rev=10152&view=rev
Author: hansonr
Date: 2008-10-26 23:26:27 +0000 (Sun, 26 Oct 2008)
Log Message:
-----------
version=11.7.6_dev # code: ScriptWindow public: sendConsoleEcho,sendConsoleMessage,notifyScriptStart,notifyScriptTermination,PdbReader
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 2008-10-26 23:25:56 UTC (rev 10151)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-10-26 23:26:27 UTC (rev 10152)
@@ -3,7 +3,7 @@
version=11.7.6_dev
-# code: ScriptWindow public: sendConsoleEcho,sendConsoleMessage,notifyScriptStart,notifyScriptTermination
+# code: ScriptWindow public: sendConsoleEcho,sendConsoleMessage,notifyScriptStart,notifyScriptTermination,PdbReader
# -----------------------------------------------------------------------------
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From: <ni...@us...> - 2009-03-22 16:00:09
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Revision: 10736
http://jmol.svn.sourceforge.net/jmol/?rev=10736&view=rev
Author: nicove
Date: 2009-03-22 15:59:59 +0000 (Sun, 22 Mar 2009)
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 2009-03-22 09:04:31 UTC (rev 10735)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2009-03-22 15:59:59 UTC (rev 10736)
@@ -1,8 +1,12 @@
# Developers: to add a description of changes you have made,
# add it on a line starting with # below the "version=..." line
-version=11.7.30
+version=11.7.31_dev
+# -----------------------------------------------------------------------------
+
+#version=11.7.30
+
# bug fix: signed applet does not use CD to set dialog default directory
# bug fix: errorCallback not functional
# new feature: set autoLoadOrientation (default: FALSE) automatically sets "reset" orientation to that in file, if present
@@ -10,6 +14,7 @@
# code: generalized setTransform() in JmolAdapter readers CSF and SpartanSmol (.spardir)
# bug fix: Spartan .spardir /input files not being read
# bug fix: draw arrow/vector slightly overshoots end point
+
# -----------------------------------------------------------------------------
#version=11.7.29
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From: <ha...@us...> - 2009-04-08 21:16:07
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Revision: 10780
http://jmol.svn.sourceforge.net/jmol/?rev=10780&view=rev
Author: hansonr
Date: 2009-04-08 21:15:31 +0000 (Wed, 08 Apr 2009)
Log Message:
-----------
version=11.7.32_dev # bug fix: Spartan SMOL file reader failure (coded & instead of && in if statement!)
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 2009-04-08 18:55:41 UTC (rev 10779)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2009-04-08 21:15:31 UTC (rev 10780)
@@ -3,6 +3,7 @@
version=11.7.32_dev
+# bug fix: Spartan SMOL file reader failure (coded & instead of && in if statement!)
# new feature: CML "isotope" and CML "partial12" bond order.
# new feature: GAMESS reader reads NBOs using
# load "xxx.gamess" filter "!EIGEN" # to only load NBOs; by default ALL MOs are loaded.
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From: <ha...@us...> - 2009-05-11 03:57:55
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Revision: 10852
http://jmol.svn.sourceforge.net/jmol/?rev=10852&view=rev
Author: hansonr
Date: 2009-05-11 03:57:46 +0000 (Mon, 11 May 2009)
Log Message:
-----------
11.7.35 VERSION
# bug fix: (applet) jmolGetPropertyAsString("image") not functional
# new feature: label %G -- group index, like atom index, 0-based for entire collection
# new feature: ramachandran DRAW -- draws dihedral planes and angles
# bug fix: draw/isosurface *name*
# bug fix: data "append" does not set model the way load "append" does
# bug fix: application frame arrows do not work after loading multiple models
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 2009-05-11 03:54:11 UTC (rev 10851)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2009-05-11 03:57:46 UTC (rev 10852)
@@ -1,7 +1,7 @@
# Developers: to add a description of changes you have made,
# add it on a line starting with # below the "version=..." line
-version=11.7.35_dev
+version=11.7.35
# bug fix: (applet) jmolGetPropertyAsString("image") not functional
# new feature: label %G -- group index, like atom index, 0-based for entire collection
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From: <ha...@us...> - 2009-07-12 04:53:59
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Revision: 11204
http://jmol.svn.sourceforge.net/jmol/?rev=11204&view=rev
Author: hansonr
Date: 2009-07-12 04:53:56 +0000 (Sun, 12 Jul 2009)
Log Message:
-----------
version=11.7.47 # new feature: navigation now does continuous motion with arrow keys;
# SPACE to stop
# LEFT/RIGHT to pan left or right
# UP/DN to move forward/back
# ALT UP/DN to pitch up/down
# CNTL UP/DN to increase/decrease speed in larger amounts
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 2009-07-12 04:50:34 UTC (rev 11203)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2009-07-12 04:53:56 UTC (rev 11204)
@@ -4,7 +4,13 @@
version=11.7.47
# code: more efficient labelGroup calculatiion
-# new feature: navigation now does continuous motion with arrow keys; space to stop
+# new feature: navigation now does continuous motion with arrow keys;
+# SPACE to stop
+# LEFT/RIGHT to pan left or right
+# UP/DN to move forward/back
+# ALT UP/DN to pitch up/down
+# CNTL UP/DN to increase/decrease speed in larger amounts
+
# bug fix: navigationmode not properly adapting with window resize or antialiasdisplay
# new feature: draw HELIX AXIS or quaternion HELIX AXIS, also for DNA/RNA
# code: cleaned up navigation business; an attempt at navigating a surface...Maybe not...
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From: <ha...@us...> - 2009-10-26 04:59:27
|
Revision: 11627
http://jmol.svn.sourceforge.net/jmol/?rev=11627&view=rev
Author: hansonr
Date: 2009-10-26 04:59:20 +0000 (Mon, 26 Oct 2009)
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 2009-10-26 04:57:16 UTC (rev 11626)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2009-10-26 04:59:20 UTC (rev 11627)
@@ -3,18 +3,15 @@
version=11.9.7_dev
-# code: reworking of JVXL reader classes, creation of JvxlCoder.java
-# code: reworking of ASimpleJvxlWriter to utilize standard classes
-# code: reworking of Parser, TextFormat, ArrayUtil, and Escape
-# to not utilize any nonstandard Java classes (such as
-# Graphics3D or BondSet or Token), thus making these
-# classes generic and not Jmol-dependent.
-#
# new feature: isosurface/pmesh commands accept unquoted file names.
# new feature: Jvxl 2.0 -- XML format for JVXL files
# here, initially, only being used for writing contour or triangle data
# NOTE -- Jvxl-XML is not backward-compatible with previous versions of Jmol.
# for now use SET testflag4 ON to enable full XML writing of JVXL files
+# new feature: Jmol frank hover provides menu tip
+# new feature: getproperty shapeinfo better reports contour levels
+# new feature: isosurface ... map CONTOUR DISCRETE [0.5, 1.0, 1.5, 2.0]
+# new feature: isosurface ... map CONTOUR INCREMENT {0.0, 1.0, 0.2}
#
# bug fix: isosurface does not clear data after functionXY or functionXYZ
# bug fix: label %vx giving x coord, not vibration x component
@@ -23,13 +20,16 @@
# bug fix: PQR reader not adaptive
# bug fix: zshade now working correctly -- not tied to slab on
# bug fix: setting spacefill to a large user-defined VDW radius incorrect
-# new feature: Jmol frank hover provides menu tip
-# new feature: getproperty shapeinfo better reports contour levels
-# new feature: isosurface ... map CONTOUR DISCRETE [0.5, 1.0, 1.5, 2.0]
-# new feature: isosurface ... map CONTOUR INCREMENT {0.0, 1.0, 0.2}
-# code: StatusListener refactored as individual class
# bug fix: Gaussian 09 LOG file reader upgrade for MOs
# bug fix: unitcell offset {1 1 1}; select UNITCELL
+#
+# code: reworking of JVXL reader classes, creation of JvxlCoder.java
+# code: reworking of ASimpleJvxlWriter to utilize standard classes
+# code: reworking of Parser, TextFormat, ArrayUtil, and Escape
+# to not utilize any nonstandard Java classes (such as
+# Graphics3D or BondSet or Token), thus making these
+# classes generic and not Jmol-dependent.
+# code: StatusListener refactored as individual class
--------------------------------------------------------------
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From: <ha...@us...> - 2010-01-28 16:15:42
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Revision: 12256
http://jmol.svn.sourceforge.net/jmol/?rev=12256&view=rev
Author: hansonr
Date: 2010-01-28 16:15:27 +0000 (Thu, 28 Jan 2010)
Log Message:
-----------
11.9.23 VERSION
# new feature: set preserveState FALSE (default TRUE) --
# for some applications it can be helpful to turn off the
# feature of preserving the state in order to save memory
# * This flag if set FALSE:
# *
# * 1) turns UNDO off for the application
# * 2) turns history off
# * 3) prevents saving of inlinedata for later LOAD "" commands
# * 4) turns off the saving of changed atom properties
# * 5) does not guarantee accurate state representation
# *
# * It is useful in situations such as web sites where
# * memory is an issue and there is no need for such.
# *
# *
# new feature: set strutsMultiple (default FALSE) allows multiple struts on a given atom
# new feature: set LOGFILE "name" -- log file will be "JmolLog_" + name
# in the Jar file directory -- note that this is not
# ever possible with the web-based version, even with the
# signed applet, but signed applet or application running
# locally can write to this file
#
# set logFile "test"
#
# new feature: LOG command -- same as print but to the log file
# can be prepended with nicely formatted date with "NOW" as the
# first three characters
#
# log "NOW\n" + getProperty("modelInfo")
#
# new feature: show state [name]
# new feature: all saved orientations now saved in state
# bug fix: isosurface ID @{xxxx} .... #ID .. #ID not overriding
# new feature: write MESH t.mesh JVXL "vertex-only" very compact style mesh surface
# new feature: isosurface SLAB {plane definition} [optional offset]
# new feature: -{plane definition} refers to opposite-facing plane as {plane definition}
# bug fix: frame *;draw {atomno=1} {atomno=5} not working properly
# bug fix: frame ALIGN for trajectories
# bug fix: isosurface vdw broken
# new feature: PDB trajectory for concatenated PDB files (no "MODEL" line)
# bug fix: pdb reader trajectory error
# bug fix: multitouch applet activation via display.hasFocus()
# working properly except you can't just jump from one
# page to another if applets are producing the SparshUI server
# be sure to go through an intermediary page, like a MAIN page
# --------------------------------------------------------------
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 2010-01-28 15:57:43 UTC (rev 12255)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-01-28 16:15:27 UTC (rev 12256)
@@ -1,7 +1,7 @@
# Developers: to add a description of changes you have made,
# add it on a line starting with # below the "version=..." line
-version=11.9.23_dev
+version=11.9.23
# new feature: set preserveState FALSE (default TRUE) --
# for some applications it can be helpful to turn off the
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From: <ha...@us...> - 2010-04-18 11:04:04
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Revision: 12887
http://jmol.svn.sourceforge.net/jmol/?rev=12887&view=rev
Author: hansonr
Date: 2010-04-18 11:03:57 +0000 (Sun, 18 Apr 2010)
Log Message:
-----------
version=12.0.RC7_dev # bug fix for parallel processing and isosurface
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 2010-04-18 11:02:58 UTC (rev 12886)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-04-18 11:03:57 UTC (rev 12887)
@@ -3,6 +3,8 @@
version=12.0.RC7_dev
+# bug fix for parallel processing and isosurface
+
# --------------------------------------------------------------
#version=12.0.RC6
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From: <ha...@us...> - 2010-09-16 03:36:12
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Revision: 14306
http://jmol.svn.sourceforge.net/jmol/?rev=14306&view=rev
Author: hansonr
Date: 2010-09-16 03:36:06 +0000 (Thu, 16 Sep 2010)
Log Message:
-----------
version=12.1.11
# test: set testFlag3 -- reports mouse action and mode (for Eric Martz)
# new feature: set multipleBondRadiusFactor 0.75
# new feature: set isosurfacePropertySmoothingPower
# 0 (no property smoothing)
# 10 (very strong smoothing)
# 7 (default, same as Jmol 11.8)
# new feature: AppletConsole allows embedding in larger applications
# new feature: smooth on-the-fly language changes in applet and application
# new feature: integrated AppConsole for embedded Jmol -- see Integration.java
# new feature: multipleBondSpacing
# set multipleBondSpacing = -1 (default, varies with viewing angle)
# set multipleBondSpacing = -0.5 (half that distance; varies with viewing angle)
# set multipleBondSpacing = 0.35 (positive ==> fixed multiple bond spacing)
# bug fix: SmarterJmolAdapter should not read zip bytes it doesn't have to
# bug fix: spacefill JMOL does not work
# bug fix: Jmol 12 does not read old 11.1 isosurface commands from states
# bug fix: load {i j k} RANGE x.x not expanding load box by 1 in each direction
# bug fix: applet console does not display startup message
# bug fix: console buttons do not change with new language
# bug fix: undo/redo problems in AppConsole
# bug fix: crystal reader can't read selected model
# bug fix: 3.5E+0.0 read as "3.5 0.0"
# bug fix: navY/navy color issue
# bug fix: write PDB for nonPDB files incorrect
# code: streamlined AppConsole and AppletConsole
# code: GuiMap/JmolConsole AbstractButton methods merged
# code: AppConsole now implements JmolStatusListener, called by JmolPanel.notifyCallback
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 2010-09-16 03:35:30 UTC (rev 14305)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-09-16 03:36:06 UTC (rev 14306)
@@ -32,7 +32,7 @@
# code: streamlined AppConsole and AppletConsole
# code: GuiMap/JmolConsole AbstractButton methods merged
-# code: AppConsole now implements JmolStatusListener, called by JmolPanel.notifyCallback
+# code: AppConsole now implements JmolCallbackListener, called by JmolPanel.notifyCallback
# --------------------------------------------------------------
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From: <ni...@us...> - 2010-11-29 19:23:11
|
Revision: 14729
http://jmol.svn.sourceforge.net/jmol/?rev=14729&view=rev
Author: nicove
Date: 2010-11-29 19:23:04 +0000 (Mon, 29 Nov 2010)
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 2010-11-29 17:17:47 UTC (rev 14728)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-11-29 19:23:04 UTC (rev 14729)
@@ -1,8 +1,12 @@
# Developers: to add a description of changes you have made,
# add it on a line starting with # below the "version=..." line
-version=12.1.24
+version=12.1.25_dev
+# --------------------------------------------------------------
+
+#version=12.1.24
+
# new feature: isosurface solvent [optionalRadius default:1.2] FULL
# FULL option does full triples-test, about 3 times slower than
# standard Jmol solvent/MOLECULAR surface, which only checks pairs.
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From: <ha...@us...> - 2011-02-06 23:55:27
|
Revision: 15132
http://jmol.svn.sourceforge.net/jmol/?rev=15132&view=rev
Author: hansonr
Date: 2011-02-06 23:55:21 +0000 (Sun, 06 Feb 2011)
Log Message:
-----------
version=12.1.34_dev
# bug fix: JavaScript getPropertyAsArray("auxiliaryInfo.models") will fail for crystal structures
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 2011-02-06 23:54:32 UTC (rev 15131)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-02-06 23:55:21 UTC (rev 15132)
@@ -4,6 +4,7 @@
version=12.1.34_dev
+# bug fix: JavaScript getPropertyAsArray("auxiliaryInfo.models") will fail for crystal structures
# bug fix: undocumented select within(hkl,...) and select within(plane,...) missing
# bug fix: message @x should replace x with a variable; "message @x is the value of x" should not
# bug fix: older syntax MESSAGE %{x} for variable value missing
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From: <ni...@us...> - 2011-04-26 21:25:50
|
Revision: 15407
http://jmol.svn.sourceforge.net/jmol/?rev=15407&view=rev
Author: nicove
Date: 2011-04-26 21:25:44 +0000 (Tue, 26 Apr 2011)
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 2011-04-26 20:33:35 UTC (rev 15406)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-04-26 21:25:44 UTC (rev 15407)
@@ -1,8 +1,12 @@
# Developers: to add a description of changes you have made,
# add it on a line starting with # below the "version=..." line
-version=12.1.44
+version=12.1.45_dev
+# --------------------------------------------------------------
+
+#version=12.1.44
+
# bug fix: MOs broken in 12.1.43
# bug fix: drawpicking fails for drawn polyhedra. (turned off for now)
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|
From: <ha...@us...> - 2011-05-09 02:19:55
|
Revision: 15442
http://jmol.svn.sourceforge.net/jmol/?rev=15442&view=rev
Author: hansonr
Date: 2011-05-09 02:19:49 +0000 (Mon, 09 May 2011)
Log Message:
-----------
version=12.1.46_dev
# bug fix: molecules incorrectly assigned for covalently attached cofactors, such as HEM (1gzx)
# TODO: This is still not quite right. It's possible that a cofactor will connect two biopolymers,
# or that two biopolymers will be connected with an S-S bond.
# In that case, we will have already created a set of independent but connected molecules
# What about hydrogen bonding?
# And we are not checking for that. Must find a way around this!
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 2011-05-09 02:13:33 UTC (rev 15441)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-05-09 02:19:49 UTC (rev 15442)
@@ -4,6 +4,12 @@
version=12.1.46_dev
# bug fix: molecules incorrectly assigned for covalently attached cofactors, such as HEM (1gzx)
+# TODO: This is still not quite right. It's possible that a cofactor will connect two biopolymers,
+# or that two biopolymers will be connected with an S-S bond.
+# In that case, we will have already created a set of independent but connected molecules
+# What about hydrogen bonding?
+# And we are not checking for that. Must find a way around this!
+
# bug fix: set picking dragMolecule then use of SHIFT after rotate COMPARE will result in unwanted translation
# --------------------------------------------------------------
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From: <ha...@us...> - 2011-07-02 16:45:12
|
Revision: 15686
http://jmol.svn.sourceforge.net/jmol/?rev=15686&view=rev
Author: hansonr
Date: 2011-07-02 16:45:05 +0000 (Sat, 02 Jul 2011)
Log Message:
-----------
version=12.1.51
# new feature: set ligandLoadFormat
# new feature: set pdbAddHydrogens
# -- for file loading
# -- adds hydrogens to ALL groups, including HET groups
# -- unlike PDB2PQR, then, ligands are properly shown
# -- also adds all multiple bonds to PDB files
# -- for altlocs you should use load option FILTER "CONF 1" (or some other specific configuration)
# -- atom numbers are appended to maximum number in file
# todo: single-element metals? -- no need to get CIF file?
# new feature: CIF reader for Ligand CIF files (e.g. http://www.rcsb.org/pdb/files/ligand/AMU.cif)
#
# new feature: calculate HYDROGEN now works for standard amino acids and nucleic acids
# -- adds "GROUP" option to connect -- puts new atoms in group of previous
# -- saves connection in state with negative first atom -- indicating that we need to assign the group
# new feature: CONTACT {xxx} MISC, and redefinition of HYDROPHOBIC
# new feature: CONTACT {xxx} VDW
# -- just maps a VDW isosurface with distances to another VDW isosurface
# new feature: LOAD command reports header/title for PDB files
# -- specifically when scriptLevel = 0 (typed entry)
# new feature: isosurface SLAB OFF -- for SLAB n, this turns that slabbing off.
# new feature: isosurface FUNCTIONXY = "x * y" and isosurface FUNCTIONXYZ = "x * x + y + z"
# -- default is from -10 to 10 every 0.25 Angstroms
# new feature: CONTACT command (Erik Wyatt/Bob Hanson 6/22/2011)
# -- creates an object of a variety of forms that
# indicates nonbonding interactions
# -- can be a planar disk perpendicular to the interaction,
# or a cigar-shaped connector
# -- HBOND (just between O and/or N)
# -- HYDROPHOBIC (not between O and/or N)
# -- percent of van der Waals distance
#
# -- works by doing a sum or difference of two complementary
# van der Waals surfaces (PLANAR) or by showing the
# intersection of the two surfaces (FULL) or by doing an NCI
# (noncovalent interaction) PROMOLECULAR calculation.
#
# -- DENSITY x.x (spot size) option does rough volume rendering.
#
#
# contact
#
# -- parameters
#
# required:
# {setA}
# optional:
# ID aaaa (if present, must be the very FIRST parameter
# ON/OFF/DELETE/LIST (if present must be the only parameter other than ID
# {setB}
# DENSITY x.x
# COLOR DENSITY
# IGNORE {ignoreSet}
# DISTANCE x.x
# PARAMETERS [....]
# FULL|PLANAR|CONNECT|NCI (FULL not implemented yet)
# HYDROPHOBIC|HBOND
# INTRAMOLECULAR|INTERMOLECULAR
# nnn%
# COLOR ...
# TRANSLUCENT/OPAQUE/MESH/NOMESH, etc... (must be last parameters)
#
# new feature: show LIGHTING
# bug fix: set defaultVDW user not working
# bug fix: _smilesString variable not being cleared when a PDB file is loaded
# code: much more efficient plane creation and mapping
# code: work on isosurface, JVXL, plane mapping
# bug fix: isosurface VDW mapping onto plane now has somewhat different coloration,
# and properly slabs to the VDW radius. This is just a SLAB option that can
# be removed like all others using isosurface SLAB NONE
# TODO: contours from saved JVXL planar isosurfaces does not seem to be correct.
# bug fix: WebMO reader fails to read HOMO/LUMO business.
# bug fix: AMU added (NAM-NAG sequences)
# bug fix: NDG added (epimer of NAG)
# bug fix: definition of CARBOHYDRATE was updated:
# -- [A2G],[NGA],[SIA],[SLB],[LBT] added (GalNAc, NeuNAc, lactose)
# -- [ASF],[NAM] removed, they are not carbohydrates
# -- a few existing ones are deprecated by PDB; they are left for compatibility
# but are now listed as such (maybe remove them in future).
# obscure bug fix: This fix: http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java?r1=13502&r2=13525
# broke Jmol reading of the Epcot hemoglobin file. Only relevant to sequential or trajectory PDB files that do not have MODEL statements.
# So then any version starting with 12.0.RC_24 (7/8/2010) through now (7/2/2011) will read the files
# correctly -- not missing the first atom -- but that messes up earlier scripts. Unfortunately the Epcot business
# (Touch-A-Molecule) was written using 12.9.23 (1/24/2010), so that is affected.
# This fix only affects states written prior to 12.0.RC_1 and just makes it so that they display correctly (though missing that one atom)
# when they involve PDB trajectories of file without MODEL records separating models. Pretty sure this is just that one file.
#
# code: Viewer passes stateScriptVersionInt on to file readers
#
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 2011-07-02 16:41:43 UTC (rev 15685)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-02 16:45:05 UTC (rev 15686)
@@ -3,6 +3,7 @@
version=12.1.51
+# new feature: set ligandLoadFormat
# new feature: set pdbAddHydrogens
# -- for file loading
# -- adds hydrogens to ALL groups, including HET groups
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|
|
From: <ha...@us...> - 2011-07-24 18:34:11
|
Revision: 15832
http://jmol.svn.sourceforge.net/jmol/?rev=15832&view=rev
Author: hansonr
Date: 2011-07-24 18:34:05 +0000 (Sun, 24 Jul 2011)
Log Message:
-----------
version=12.2.RC1
# RELEASE CANDIDATE 1 for Jmol 12.2
# new feature: Surface Tool GUI -- just slicing so far and does all surfaces rather
# then selected. (Jonathan Gutow)
# new feature: select within(x.x, VDW, aaaa)
# -- selects atoms that have overlapping VDW surfaces with set aaaa
# -- if x.x is present, BOTH interacting atom radii are adjusted:
# -- if x.x > 10, then this is assumed to be a percent, such as 110%, 100%, 90%
# -- if x.x <= 10, then this is assumed to be a distance to be added to the VDW radii
# -- so, for example, select within(1.4, VDW, aaaa) selects groups with overlapping solvent-accessible surfaces
# new feature: getProperty isosurfaceInfo
# -- includes vertexCount, polygonCount, vertices, vertexValues, and polygons
# new feature: isosurface atomicOrbital <n> <l> <m> <z> POINTS <radius> <seed>
# -- new default cutoff of 0.04 corresponds to factoring in 1/2sqrtPI
# -- <radius> is new
# -- must be a decimal number to distinguish it from the seed.
# -- specifies a given radius
# bug fix: isosurface slab of isosurface MO causes null pointer exception
# bug fix: isosurface slab translucent of translucent isosurfaces causes problems
# -- isosurface slab translucent ---> will now turn isosurface opaque first
# -- isosurface slab translucent without a color ---> will now take on current color of isosurface rather than white
# -- color isosurface translucent of translucent-slabbed isosurface will remove ALL slabbing
# bug fix: WebExport not getting Jmol Icon for title bar.
# bug fix: PDB reader may read bfactors off by 0.01
# bug fix: NWChem reader without input deck but with frequencies fails to load
# bug fix: 12.1.51 breaks isosurface... colorscheme...
# bug fix: isosurface slab -@xxxx... will negate variable xxxx if it is a plane
# bug fix: contact {setA} {setB} should not allow overall of setA and setB unless NCI.
# bug fix: contact FULL set to minimum resolution 10 (pairwise)
# bug fix: isosurface intersection .... function "..." ignores function and just does "a-b"
# code: super-fast "micro-isosurface" merging for CONTACT. Wow!
# -- set pdbAddHydrogens; load =2bxa; contact {:A} {:A}
# -- merges 2341 microisosurfaces in 325 ms on BH laptop!
# code: fast pointilist atomic orbitals. THANK YOU, Pshemak Maslak, Brian Hardock, Rob Caldwell, and Tom Stitt!
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 2011-07-24 18:29:24 UTC (rev 15831)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-24 18:34:05 UTC (rev 15832)
@@ -1,31 +1,18 @@
# Developers: to add a description of changes you have made,
# add it on a line starting with # below the "version=..." line
-version=12.1.52_dev
+version=12.2.RC1
-# code: super-fast "micro-isosurface" merging for CONTACT. Wow!
-# -- set pdbAddHydrogens; load =2bxa; contact {:A} {:A}
-# -- merges 2341 microisosurfaces in 325 ms on BH laptop!
-# bug fix: isosurface slab of isosurface MO causes null pointer exception
-# bug fix: isosurface slab translucent of translucent isosurfaces causes problems
-# -- isosurface slab translucent ---> will now turn isosurface opaque first
-# -- isosurface slab translucent without a color ---> will now take on current color of isosurface rather than white
-# -- color isosurface translucent of translucent-slabbed isosurface will remove ALL slabbing
+# RELEASE CANDIDATE 1 for Jmol 12.2
+
# new feature: Surface Tool GUI -- just slicing so far and does all surfaces rather
-# then selected.
-# bug fix: WebExport not getting Jmol Icon for title bar.
-# bug fix: PDB reader may read bfactors off by 0.01
-# bug fix: NWChem reader without input deck but with frequencies fails to load
-# bug fix: 12.1.51 breaks isosurface... colorscheme...
+# then selected. (Jonathan Gutow)
# new feature: select within(x.x, VDW, aaaa)
# -- selects atoms that have overlapping VDW surfaces with set aaaa
# -- if x.x is present, BOTH interacting atom radii are adjusted:
# -- if x.x > 10, then this is assumed to be a percent, such as 110%, 100%, 90%
# -- if x.x <= 10, then this is assumed to be a distance to be added to the VDW radii
# -- so, for example, select within(1.4, VDW, aaaa) selects groups with overlapping solvent-accessible surfaces
-# bug fix: isosurface slab -@xxxx... will negate variable xxxx if it is a plane
-# bug fix: contact {setA} {setB} should not allow overall of setA and setB unless NCI.
-# bug fix: contact FULL set to minimum resolution 10 (pairwise)
# new feature: getProperty isosurfaceInfo
# -- includes vertexCount, polygonCount, vertices, vertexValues, and polygons
# new feature: isosurface atomicOrbital <n> <l> <m> <z> POINTS <radius> <seed>
@@ -33,9 +20,26 @@
# -- <radius> is new
# -- must be a decimal number to distinguish it from the seed.
# -- specifies a given radius
-# code: superfast atomic orbitals. THANK YOU, Pshemak Maslak, Brian Hardock, Rob Caldwell, and Tom Stitt!
+
+# bug fix: isosurface slab of isosurface MO causes null pointer exception
+# bug fix: isosurface slab translucent of translucent isosurfaces causes problems
+# -- isosurface slab translucent ---> will now turn isosurface opaque first
+# -- isosurface slab translucent without a color ---> will now take on current color of isosurface rather than white
+# -- color isosurface translucent of translucent-slabbed isosurface will remove ALL slabbing
+# bug fix: WebExport not getting Jmol Icon for title bar.
+# bug fix: PDB reader may read bfactors off by 0.01
+# bug fix: NWChem reader without input deck but with frequencies fails to load
+# bug fix: 12.1.51 breaks isosurface... colorscheme...
+# bug fix: isosurface slab -@xxxx... will negate variable xxxx if it is a plane
+# bug fix: contact {setA} {setB} should not allow overall of setA and setB unless NCI.
+# bug fix: contact FULL set to minimum resolution 10 (pairwise)
# bug fix: isosurface intersection .... function "..." ignores function and just does "a-b"
+# code: super-fast "micro-isosurface" merging for CONTACT. Wow!
+# -- set pdbAddHydrogens; load =2bxa; contact {:A} {:A}
+# -- merges 2341 microisosurfaces in 325 ms on BH laptop!
+# code: fast pointilist atomic orbitals. THANK YOU, Pshemak Maslak, Brian Hardock, Rob Caldwell, and Tom Stitt!
+
# --------------------------------------------------------------
#version=12.1.51
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|
|
From: <ha...@us...> - 2011-08-09 18:15:33
|
Revision: 15959
http://jmol.svn.sourceforge.net/jmol/?rev=15959&view=rev
Author: hansonr
Date: 2011-08-09 18:15:27 +0000 (Tue, 09 Aug 2011)
Log Message:
-----------
it's fine -- do release, please
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 2011-08-09 18:13:33 UTC (rev 15958)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-08-09 18:15:27 UTC (rev 15959)
@@ -1,7 +1,7 @@
# Developers: to add a description of changes you have made,
# add it on a line starting with # below the "version=..." line
-version=12.2.RC3_HOLD
+version=12.2.RC3
# new feature: selection of surfaces in SurfaceTool
# bug fix: color broken in 12.2.RC2
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|
|
From: <ni...@us...> - 2011-11-15 03:23:32
|
Revision: 16470
http://jmol.svn.sourceforge.net/jmol/?rev=16470&view=rev
Author: nicove
Date: 2011-11-15 03:23:26 +0000 (Tue, 15 Nov 2011)
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 2011-11-14 20:45:09 UTC (rev 16469)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-11-15 03:23:26 UTC (rev 16470)
@@ -1,8 +1,12 @@
# Developers: to add a description of changes you have made,
# add it on a line starting with # below the "version=..." line
-version=12.3.5
+version=12.3.6_dev
+# =============================================================================
+
+#version=12.3.5
+
# new feature: color isosurface PHASE color1 color2
# -- allows post-isosurface creation coloring by phase (atomicOrbitals)
# bug fix: isosurface scale 0.5 plane... broken if no atoms present
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|
From: <ni...@us...> - 2012-03-05 19:15:11
|
Revision: 16862
http://jmol.svn.sourceforge.net/jmol/?rev=16862&view=rev
Author: nicove
Date: 2012-03-05 19:15:04 +0000 (Mon, 05 Mar 2012)
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 2012-03-05 12:01:58 UTC (rev 16861)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-03-05 19:15:04 UTC (rev 16862)
@@ -1,8 +1,12 @@
# Developers: to add a description of changes you have made,
# add it on a line starting with # below the "version=..." line
-version=12.3.17
+version=12.3.18_dev
+# =============================================================================
+
+#version=12.3.17
+
# new feature: (JspecView 2.0.10033) new script commands (indicated with *)
# UNKNOWN("?"),
# APPLETID("APPLETID"),
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From: <ni...@us...> - 2012-08-09 17:39:02
|
Revision: 17442
http://jmol.svn.sourceforge.net/jmol/?rev=17442&view=rev
Author: nicove
Date: 2012-08-09 17:38:55 +0000 (Thu, 09 Aug 2012)
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 2012-08-09 16:37:04 UTC (rev 17441)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-08-09 17:38:55 UTC (rev 17442)
@@ -7,8 +7,12 @@
# Don't use ___ in your text, as that is the key for stripping out
# the information saved in the JAR version of this file.
-___version=13.0.RC4
+___version=13.0.RC5_dev
+=============================================================================
+
+version=13.0.RC4
+
new feature: write SCENE PNG|PNGJ "xxxx.spt" option to create PNG or PNGJ files (same file, just different extension)
new feature: "menu" as sole contents of a script pops up the context menu
-- joins category of special commands, including "exit" "pause" and "quit"
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|
From: <ni...@us...> - 2012-08-14 17:34:38
|
Revision: 17455
http://jmol.svn.sourceforge.net/jmol/?rev=17455&view=rev
Author: nicove
Date: 2012-08-14 17:34:32 +0000 (Tue, 14 Aug 2012)
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 2012-08-13 23:19:11 UTC (rev 17454)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-08-14 17:34:32 UTC (rev 17455)
@@ -7,8 +7,12 @@
# Don't use ___ in your text, as that is the key for stripping out
# the information saved in the JAR version of this file.
-___version=13.0.RC6
+___version=13.0.RC7_dev
+=============================================================================
+
+version=13.0.RC6
+
bug fix: Gaussian reader not reading "AO basis set in the form of general basis input" properly ("Gen" keyword)
bug fix: Gaussian reader not reading "7D 0" correctly
bug fix: Trajectories still broken for PDB files
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|
From: <ni...@us...> - 2012-10-17 16:36:58
|
Revision: 17668
http://jmol.svn.sourceforge.net/jmol/?rev=17668&view=rev
Author: nicove
Date: 2012-10-17 16:36:48 +0000 (Wed, 17 Oct 2012)
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 2012-10-17 15:22:58 UTC (rev 17667)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-10-17 16:36:48 UTC (rev 17668)
@@ -7,8 +7,12 @@
# Don't use ___ in your text, as that is the key for stripping out
# the information saved in the JAR version of this file.
-___version=13.1.7
+___version=13.1.8_dev
+=============================================================================
+
+version=13.1.7
+
FEATURE CHANGE: getProperty isosurfaceInfo no longer returns vertex data
new feature: getProperty isosurfaceData returns vertex data
new feature: set cartoonFancy -- creates elliptical ribbon for cartoons
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