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Questions and answers => RNA structures (DSSR) => Topic started by: gabriellecaponigro on February 03, 2017, 02:20:17 pm

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Title: PyMOL Mac error
Post by: gabriellecaponigro 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.

Title: Re: PyMOL Mac error
Post by: xiangjun 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

Title: Re: PyMOL Mac error
Post by: speleo3 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

Title: Re: PyMOL Mac error
Post by: xiangjun 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 (https://pymolwiki.org/index.php/Dssr_block)" PyMOLWiki page.

Best regards,

Xiang-Jun

Title: Re: PyMOL Mac error
Post by: gabriellecaponigro 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] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.