Or, just use 11.8.18 -- changes since then:
#version=11.8.21
# bug fix: black shades lost in writing (antialiased) images
# bug fix: using --i instead of i-- with for causes infinite loop
# bug fix: draw FIXED arc, curve, arrow -- no reason not to do this, I
think.
# bug fix: spacegroup 177 must not have Hall symbol P 63 same as H-M symbol
P 63
#
-----------------------------------------------------------------------------
#version=11.8.20
# bug fix: hbonds after wireframe will be thin
# bug fix: lcaocartoon "s" is not being saved in state
# bug fix: All water should be included in the 'solvent' set
#
-----------------------------------------------------------------------------
#version=11.8.19
# bug fix: GROMACS reader should not require forces
# bug fix: select IONS broken (left broken in 11.6)
# bug fix: load models {(.....)} not preserved in state
# bug fix: structure HELIX {3-4} will cause 5-... to lose structure type
# bug fix: select 1:3.*
# bug fix: [state] button in app console not showing state
# bug fix: load sometimes not properly accounting for unique axis
information
# bug fix: write frame typed in application can hang Jmol.
# bug fix: refresh after echo @{...} causes Jmol to hang.
On Thu, Mar 18, 2010 at 2:27 PM, Robert Hanson <[email protected]> wrote:
> yes, Jmol 11.8.21 bug doesn't allow SPACEGROUP designation in LOAD command.
> Fixed for 11.8.22; not a problem for 11.9 -- consider using that for now
> until 11.8.22 is released next week (probably).
>
> Bob
>
>
> On Thu, Mar 18, 2010 at 11:27 AM, Ian Thomas <[email protected]>wrote:
>
>> Hello,
>>
>> I have been using Jmol v11.8.13 since December with no issues. Yesterday I
>> tried updating to v11.8.21 and now I have an issue that prevents me from
>> displaying the unit cell of a structure loaded from a Mol2 file. Nothing
>> else has changed.
>>
>> Here is the Java console error output I now get:
>>
>> ----
>> FileManager.getAtomSetCollectionFromFile(http://frog/temp/ABENAX.mol2) //
>> http://frog/temp/ABENAX.mol2
>> FileManager opening http://frog/temp/ABENAX.mol2
>> The Resolver thinks Mol2
>> java.lang.ArrayIndexOutOfBoundsException: 2
>> at org.jmol.symmetry.SpaceGroup.buildSpaceGroup(Unknown Source)
>> at org.jmol.symmetry.SpaceGroup.<init>(Unknown Source)
>> at org.jmol.symmetry.SpaceGroup.createSpaceGroup(Unknown Source)
>> at org.jmol.symmetry.SpaceGroup.createSpaceGroup(Unknown Source)
>> at org.jmol.symmetry.Symmetry.createSpaceGroup(Unknown Source)
>> at
>> org.jmol.adapter.smarter.AtomSetCollectionReader.applySymmetryAndSetTrajectory(Unknown
>> Source)
>> at org.jmol.adapter.readers.more.Mol2Reader.processMolecule(Unknown
>> Source)
>> at
>> org.jmol.adapter.readers.more.Mol2Reader.readAtomSetCollection(Unknown
>> Source)
>> at
>> org.jmol.adapter.smarter.AtomSetCollectionReader.readData(Unknown Source)
>> at
>> org.jmol.adapter.smarter.Resolver.getAtomCollectionAndCloseReader(Unknown
>> Source)
>> at
>> org.jmol.adapter.smarter.SmarterJmolAdapter.staticGetAtomSetCollectionFromReader(Unknown
>> Source)
>> at
>> org.jmol.adapter.smarter.SmarterJmolAdapter.getAtomSetCollectionFromReader(Unknown
>> Source)
>> at
>> org.jmol.viewer.FileManager$FileReaderThread.createAtomSetCollection(Unknown
>> Source)
>> at org.jmol.viewer.FileManager$FileReaderThread.run(Unknown Source)
>> at
>> org.jmol.viewer.FileManager.createAtomSetCollectionFromFile(Unknown Source)
>> at org.jmol.viewer.Viewer.openFile(Unknown Source)
>> at org.jmol.viewer.ScriptEvaluator.load(Unknown Source)
>> at org.jmol.viewer.ScriptEvaluator.instructionDispatchLoop(Unknown
>> Source)
>> at org.jmol.viewer.ScriptEvaluator.evaluateCompiledScript(Unknown
>> Source)
>> at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source)
>> at
>> org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(Unknown Source)
>> at
>> org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown
>> Source)
>> at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown
>> Source)
>> at java.lang.Thread.run(Unknown Source)
>> file ERROR: http://frog/temp/ABENAX.mol2
>> Unexpected end of file after line 60:
>> 8.4590 16.9420 6.6832 90.0000 96.9290 90.0000 14 1
>> for file http://frog/temp/ABENAX.mol2
>> type mol2
>> openFile(http://frog/temp/ABENAX.mol2): 62 ms
>> eval ERROR: Unexpected end of file after line 60:
>> 8.4590 16.9420 6.6832 90.0000 96.9290 90.0000 14 1
>> for file http://frog/temp/ABENAX.mol2
>> type mol2
>> ----
>> load "" { 1 1 1 } spaceGroup
>> "x,y,z;x,1/2-y,1/2+z;-x,-y,-z;-x,1/2+y,1/2-z" unitcell { 8.459 16.942 6.6832
>> 90 96.929 90 >> } <<
>> ----
>>
>>
>> I have attached the Mol2 file in question to this email for reference.
>> This error now happens for every single Mol2 file I try, so I don't think
>> there is anything special about this particular structure/file.
>>
>> I should point out that just loading the file into Jmol without displaying
>> the unit cell still works fine as before. In addition, I have just tried
>> exactly the same tests using the latest Jmol v11.9.33 and that works fine in
>> every way including displaying the unit cell.
>>
>> Does anyone know what has changed between v11.8.13 and v11.8.21 that might
>> explain this problem? Is this likely to be resolved on the v11.8.* branch,
>> or do I need to move over to the new v11.9.* branch straight away to avoid
>> this issue? How long will it be until v11.9.* becomes the official release
>> branch?
>>
>> Thanks in advance for your help,
>>
>> Ian Thomas
>>
>>
>> --
>> Ian Thomas
>> Senior Scientific Software Engineer
>> CCDC
>>
>>
>>
>>
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>>
>>
>> ------------------------------------------------------------------------------
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>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
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