Hello-
I have successfully (I think) run the APBS and ISIM calculations using the ISIM interface for the small protein Barstar (PDB ID 1A19), using ion concentrations of 150 mM Cl-, 50 mM Mg2+, and 50 mM Na+.
I can view my results, however when I select "3D Pymol View" I only get a black pymol screen, and no data or protein shows up. Have you encountered any problems like this before?
I've included my results, and the pymol portion of the log file below.
Please let me know if you have any suggestions-
Thank you!
Rachel Rice
Nathan Baker Lab
Washington University in St. Louis
Here are my results for Ion Counts:
Cl (-1) 150.0 mM 3.0 Å 33.0 ions -5.7 ions 27.3 ± 3.3 ions
Mg (+2) 50.0 mM 3.0 Å 11.0 ions 2.7 ions 13.7 ± 2.0 ions
Na (+1) 50.0 mM 3.0 Å 11.0 ions 1.1 ions 12.1 ± 2.5 ions
And here is what the log file says when I try to run pymol:
Running Pymol thread
RunPymolThread Starting Pymol task...
RunPymolThread Unpacking Pymol executable from
<dir_pymol/pymol_arguments> to
</tmp/ISIM43188/working>
RunPymolThread Unpacked Pymol executable.RunPymolThread Osname=Mac
getPymolLocation: begin
getMuffinContents: begin
getMuffinContents: URL <http://public.simtk.org> mot found: /Users/rlrice/Library/Caches/Java/cache/javaws/muffins/http/Dpublic.simtk.org/P80/PU (No such file or directory)
No muffin avalaible for URL=<http://public.simtk.org>getPymolLocation: No muffin or muffin location invalid.
checkForPymolBasedOnOsTrying File=<MacPyMOL>
Checking directory=</Applications/MacPyMOL.app/Contents/MacOS>Directory=</Applications/MacPyMOL.app/Contents/MacOS> exists.
Is Valid directory/file
getPymolLocation:Mac
getPathToPymolExecutable: begin
RunPymolThread Pymol executable path=</Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL>
RunPymolThread Pymol environment path=</Applications/MacPyMOL.app/pymol>
RunPymolThread Python environment path=</Applications/MacPyMOL.app/pymol/ext>
RunPymolThread No. arguments=3
Issuing Pymol command=< /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -iFmq /tmp/ISIM43188/working/run.py>
Setting environment variables CWD and PWDEnvironment variable settings
USER=rlrice
SECURITYSESSIONID=4945c0
JAVA_MAIN_CLASS_415=com.sun.javaws.Main
APP_NAME_415=Ion Simulator Interface
HOME=/Users/rlrice
PWD=/tmp/ISIM43188/working
CWD=/tmp/ISIM43188/working
__CF_USER_TEXT_ENCODING=0x1F5:0:0
SHELL=/bin/bash
PATH=/usr/bin:/bin:/usr/sbin:/sbin
Issuing command: </Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -iFmq /tmp/ISIM43188/working/run.py >
Issued command