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
caffeine.pdb
Description: Protein Databank data
caffeine.xyz
Description: Protein Databank data
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