Hi Bob, It works great now!
Thanks, Oliver (btw.: How was your presentation in Redmond? ) On Thu, Feb 10, 2011 at 14:50, Robert Hanson <hans...@stolaf.edu> wrote: > Not intended; just never tested. > > version=12.1.35_dev > version=12.0.30_dev > > # bug fix: application with file name does not run jmolscript: embedded > scripts > > see http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip > > > > On Thu, Feb 10, 2011 at 2:56 PM, Oliver Stueker > <revilo2...@users.sourceforge.net> wrote: >> >> Hi, >> >> Though I mentioned to this issue before, it's probably better to start >> a new thread for this: >> >> When I load a molecule with an embedded jmolscript to the >> Jmol-application directly via the command line, the embedded script is >> not executed. >> >> for example: >> I take caffeine.xyz from >> http://chemapps.stolaf.edu/jmol/docs/examples-12/data/caffeine.xyz >> and modify the comment line by adding: jmolscript: selectionHalos on; >> select nitrogens ; >> (attached) >> >> When I now in a terminal window run: >> jmol caffeine.xyz >> >> Jmol starts, loads the molecule but doesn't execute the embedded script. >> >> If however I load the file after the Jmol-application was started >> (e.g. by load "caffeine.xyz" or via the File Open dialogue) the >> embedded script is executes just as expected. >> >> Question: Is this behaviour intended? If yes: Why? >> >> >> >> >> If not intended: Here's some information that might help tracking down >> the issue: >> >> * I was able to reproduce this with several Jmol versions between >> 12.0.11 and 12.1.35_dev. >> >> * I have tested this with XYZ and PDB Formats ( test files attached ) >> >> * I was able to reproduce this under Linux and Windows with Sun >> (Oracle) Java 1.6.0_22 >> - ~/local/jmol/jmol-12.1.35_dev contains the latest Jmol.jar >> - ~/local/jmol/jmol-12.1.34 contains the latest shell and batch >> scripts jmol, jmol.sh and jmol.bat (from binary-tar.gz distribution) >> >> - commands under Linux: >> export JMOL_HOME=${HOME}/local/jmol/jmol-12.1.35_dev >> cd ~/tests >> ~/local/jmol/jmol-12.1.34/jmol caffeine.pdb >> # or alternative: ~/local/jmol/jmol-12.1.34/jmol.sh caffeine.pdb >> >> - commands under Windows: >> set JMOL_HOME=Z:\local\jmol\jmol-12.1.35_dev >> set PATH=Z:\local\jmol\jmol-12.1.34;%PATH% >> z: >> cd tests >> jmol.bat caffeine.pdb >> >> * The output looks normal except the fact that the neglected script is >> echoed to the shell (the line after "The Resolver thinks"): >> ... >> FileManager.getAtomSetCollectionFromFile(caffeine.pdb) >> FileManager opening /home/stuekero/tests/caffeine.pdb >> The Resolver thinks Pdb >> #jmolScript: selectionHalos on; select nitrogens ; >> openFile(caffeine.pdb): 99 ms >> reading 24 atoms >> ... >> >> This happens on both Windows and Linux and with XYZ and PDB. >> >> Thanks, >> Oliver >> >> > > > > -- > 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 > ------------------------------------------------------------------------------ The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
