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Author Topic: PyMOL Mac error  (Read 679 times)

Offline gabriellecaponigro

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PyMOL Mac error
« on: February 03, 2017, 02:20:17 pm »
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.
« Last Edit: February 03, 2017, 02:29:56 pm by gabriellecaponigro »

Offline xiangjun

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Re: PyMOL Mac error
« Reply #1 on: February 03, 2017, 03:36:28 pm »
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:

Code: [Select]
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

Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline speleo3

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Re: PyMOL Mac error
« Reply #2 on: February 03, 2017, 03:57:55 pm »
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:

Code: [Select]
PyMOL>import os
PyMOL>print os.getenv('PATH')

Thomas

Offline xiangjun

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Re: PyMOL Mac error
« Reply #3 on: February 03, 2017, 04:12:13 pm »
Hi Thomas,

Thank you so much for your quick response. You may want to add a note for Mac users in the "Dssr block" PyMOLWiki page.

Best regards,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline gabriellecaponigro

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Re: PyMOL Mac error
« Reply #4 on: February 10, 2017, 11:17:23 am »
Hello,

This did fix the issue. Thank you so much.

Gabrielle

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.