Dear Developers I am trying to build a chimera integrated python script to energy minimize protein pdb files. I have a list of ~400 pdb files (clean homology models) which I need to Energy minimize Can you please help me with this matter: like how to select files from directory adding H-atoms selecting the forcefield, etc how can I automate this whole process ? Thank you, I would appreciate all your help. Ajay -- Ajay Pal PhD Research Student Dublin Institute of Technology, Dublin -- This email originated from DIT. If you received this email in error, please delete it from your system. Please note that if you are not the named addressee, disclosing, copying, distributing or taking any action based on the contents of this email or attachments is prohibited. www.dit.ie Is ó ITBÁC a tháinig an ríomhphost seo. Má fuair tú an ríomhphost seo trí earráid, scrios de do chóras é le do thoil. Tabhair ar aird, mura tú an seolaí ainmnithe, go bhfuil dianchosc ar aon nochtadh, aon chóipeáil, aon dáileadh nó ar aon ghníomh a dhéanfar bunaithe ar an ábhar atá sa ríomhphost nó sna hiatáin seo. www.dit.ie Tá ITBÁC ag aistriú go Gráinseach Ghormáin – DIT is on the move to Grangegorman <http://www.dit.ie/grangegorman>
Hi Ajay, My advice is to first figure out exactly which Chimera commands you want to use for each structure. You would do that by entering the commands manually in the Command Line (show Command Line using Favorites menu) to try them. The relevant commands are “open" “addh” “addcharge” “minimize” and “write” which all have various options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/open.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> Then, after you have figured out the desired commands/options, see this page for how to use script looping through multiple structures. <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.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 Jan 20, 2017, at 3:53 AM, Ajay Pal <d16124207@mydit.ie> wrote:
Dear Developers I am trying to build a chimera integrated python script to energy minimize protein pdb files.
I have a list of ~400 pdb files (clean homology models) which I need to Energy minimize Can you please help me with this matter: like how to select files from directory adding H-atoms selecting the forcefield, etc how can I automate this whole process ?
Thank you, I would appreciate all your help. Ajay
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Ajay Pal -
Elaine Meng