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Author Topic: How to make blocview -i work with pymol in batch mode.  (Read 4216 times)

Offline mauricio esguerra

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How to make blocview -i work with pymol in batch mode.
« on: May 20, 2009, 02:45:48 pm »
Hi Xiang-Jun,

Recently I was using blocview with the -i option to produce ray traced images of a large number of RNA base-steps and found that every time pymol was called, it opened a new OpenGL window (a bit annoying for 100+ molecules).

I thought it would be useful to mention here that to send the OpenGL window to the "background", one just has to alter line 30 of the x3dna_r3d2png script located in the /bin directory of X3DNA to read:

system("pymol -qc $pmlfile 2&> x3dna_r3d_pymol.msg");

instead of

system("pymol $pmlfile 2&> x3dna_r3d_pymol.msg");

Notice that you only need to add -qc after the pymol command.

Hope this helps someone, and thanks for 3DNA Xiang-Jun.

Offline xiangjun

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Re: How to make blocview -i work with pymol in batch mode.
« Reply #1 on: May 20, 2009, 07:03:35 pm »
Hi Mauricio,

Thanks for your note. In the current version of v2.0, the system call is as follows:
Code: [Select]
system("pymol -c $pmlfile 2&> x3dna_r3d_pymol.msg");i.e., with the -c option to run pymol in command-line mode. If I remember it correctly, I added this -c option following your suggestion (thanks!),  while you and Guohui helped verifying the recipes for the 2008 3DNA Nature Protocols paper.

I understand what -q means, and could add it to 3DNA v2.0 as you suggested (i.e., -qc). Does it really matter? What differences does it make: -c vs -qc? Could you have a try and report back?

While 3DNA is distributed in binary form for C programs (per Rutgers license policy), the Perl scripts are actually open source. It has been my intention to keep it that way so that users can follow the examples, make changes as needs arise, and create new tools.



Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.