[chimera-dev] Fwd: [Chimera-users] Working with several proteins

Elaine Meng meng at cgl.ucsf.edu
Wed Apr 16 15:33:31 PDT 2014

Begin forwarded message:

> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Working with several proteins
> Date: April 16, 2014 3:16:07 PM PDT
> To: Navya Shilpa Josyula <njosyu2 at uic.edu>
> Cc: chimera-users at cgl.ucsf.edu
> Reply-To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>, "chimera-dev at cgl.ucsf.edu" <chimera-dev at cgl.ucsf.edu>
> Dear Navya,
> This would require Python programming because not all of these tasks can be done with Chimera commands. See the Chimera programmer's guide:
> <http://www.rbvi.ucsf.edu/chimera/current/docs/ProgrammersGuide/index.html>
> You did not say if your structures are from the PDB database or whether you generated them somehow (for example, from a simulation).  If they are in the PDB database, it is possible they are also in the CASTp database, in which case you could open each with a Chimera command something like:
> open castp:2gbp
> CASTp finds a lot of pockets for one structure, and each pocket would have a separate volume value and list of residues.   
> <http://www.rbvi.ucsf.edu/chimera/current/docs/UsersGuide/castp.html#pocketlist>
> If the structures are not in the CASTp database, you would have to upload them individually for a calculation at the CASTp web server, and this cannot be done from inside Chimera.  After you got the CASTp results by email, you could open them in Chimera.  Even if the structure is already in CASTp, it might just be better to get the CASTp results files directly from their website and not use Chimera. If showing CASTp results in Chimera, you would then have to use python to write out the desired information to a file anyway.
> CASTp search at their website:
> <http://sts-fw.bioengr.uic.edu/castp/index.php>
> CASTp upload for new structure calculation:
> <http://sts-fw.bioengr.uic.edu/castp/calculation.php>
> For bfactor, again you can just get the values directly from the text of the PDB files, no need to go through Chimera.  Just like for CASTp, it may be simpler to write your own scripts to get the values from these files.
> Back to Chimera:  To calculate areaSAS you have to show the surface (for example, command: surface).  Attribute values can be written out to a file using the File menu of the Render by Attribute tool (in menu under Tools… Depiction), 
> <http://www.rbvi.ucsf.edu/chimera/current/docs/ContributedSoftware/render/render.html#saving>
> ...but again to process many structures instead of using the GUI, you would have to use python scripting because there isn't a command.  There is a similar script attached to this previous post (get the writeAttr.py attachment using the URL near the bottom, unfortunately it will be named attachment.bin but it is really a text file containing the script):
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003531.html>
> Best,
> 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 Apr 15, 2014, at 7:29 PM, Navya Shilpa Josyula <njosyu2 at uic.edu> wrote:
>> Hi,
>> I am working on a set of 400 proteins and for all these proteins I have specific list of amino acid residues. I wanted to know if there is any available script or a command to get the following
>> 	• atomic areaSAS 
>> 	• atomic B-factor values
>> 	• CASTp identified pocket residues and 
>> 	• CASTp identified pocket volumes 
>> for all the residues of these 400 proteins to be written in a single file. Kindly help me at your earliest.
>> Thank you in advance for your help.
>> Regards,
>> Navya
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