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I am trying to run and use dssr_block for PyMOL on a Mac.
I am able to run the python file, but when I try to use the dssr_block command, I get the error
Error: Error: Cannot execute exe="x3dna-dssr"
How would I be able to fix this in order to use the dssr_block functions?
Just to clarify, DSSR is installed, and x3dna-dssr is in the PATH.
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Hi,
It is hard me to know exactly where the problem could be. However, could you please verify the following to ensure that you have both DSSR and PyMOL installed properly:
x3dna-dssr -i=1ehz.pdb --cartoon-block -o=1ehz.pml
# Then within PyMOL, @1ehz.pml -- you should see the cartoon-block image
You may want to ask this question on the PyMOL mailing list. I am also notifying Thomas Holder (who wrote the plug-in) about this issue.
Best regards,
Xiang-Jun
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Hi Gabrielle,
I get the same error with the following setup:
- $PATH modified in ~/.bashrc to include x3dna-dssr directory
- launching MacPyMOL from the dock, which unfortunately doesn't read my ~/.bashrc
The following setups work:
- launch /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL from a terminal
- copy x3dna-dssr to /usr/bin and launch MacPyMOL from dock
- modify os.environ["PATH"] in ~/.pymolrc
Hope one of these options work for you.
You can verify PATH on the PyMOL command line:
PyMOL>import os
PyMOL>print os.getenv('PATH')
Thomas
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Hi Thomas,
Thank you so much for your quick response. You may want to add a note for Mac users in the "Dssr block (https://pymolwiki.org/index.php/Dssr_block)" PyMOLWiki page.
Best regards,
Xiang-Jun
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Hello,
This did fix the issue. Thank you so much.
Gabrielle
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University