trying to process 1000 proteins via Chimera
Hello, We are Chimera users trying to process 1000 proteins, e.g., add hydrogen and charge. We want to do this via a Chimera for DOCK preparation. I know that Chimera accepts command line, but this is not realizable for processing 10000 molecules. Have you any idea of the task? Thanks! Jian Chen
Hi Jian, There is no "dock prep" command, but there are commands "addh" and "addcharge": <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html> Some other parts of Dock Prep can also be done with commands (for example "delete solvent"), but python scripting may be required for certain steps if you need them. I cannot advise on the python part, perhaps others can. For scripting to handle multiple structures, please see previous posts such as: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/ 003261.html> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/ 003262.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 20, 2009, at 5:51 PM, Bisn wrote:
Hello, We are Chimera users trying to process 1000 proteins, e.g., add hydrogen and charge. We want to do this via a Chimera for DOCK preparation. I know that Chimera accepts command line, but this is not realizable for processing 10000 molecules. Have you any idea of the task? Thanks! Jian Chen
Hi Jian, In addition there is a previous post on the chimera-dev list that is specifically germane to your request: http://www.cgl.ucsf.edu/pipermail/chimera-dev/2009/000634.html Let me know if the info in that isn't enough for what you want to do. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Oct 21, 2009, at 10:07 AM, Elaine Meng wrote:
Hi Jian, There is no "dock prep" command, but there are commands "addh" and "addcharge": <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html>
Some other parts of Dock Prep can also be done with commands (for example "delete solvent"), but python scripting may be required for certain steps if you need them. I cannot advise on the python part, perhaps others can.
For scripting to handle multiple structures, please see previous posts such as: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003261.html
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003262.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 20, 2009, at 5:51 PM, Bisn wrote:
Hello, We are Chimera users trying to process 1000 proteins, e.g., add hydrogen and charge. We want to do this via a Chimera for DOCK preparation. I know that Chimera accepts command line, but this is not realizable for processing 10000 molecules. Have you any idea of the task? Thanks! Jian Chen
participants (3)
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Bisn -
Elaine Meng -
Eric Pettersen