[Chimera-users] CASTp data

Elaine Meng meng at cgl.ucsf.edu
Mon Jun 9 17:22:22 PDT 2014


Hi,
The ones "from Chimera" aren't calculated in Chimera, they are just results fetched from the CASTp database, as described:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/castp.html>

In that case they should be the same as querying the CASTp database directly:
<http://sts-fw.bioengr.uic.edu/castp/index.php>

I wouldn't know why that might give you a different result than using their server
<http://sts-fw.bioengr.uic.edu/castp/calculation.php>
Some possibilities are differences in handling of multimeric state or things like het residues, or whether the PDB entry has itself changed over time.  You might ask the CASTp authors if you get two different results from their database and their new-calculation server.

There is some possibility, however, that you had fetched an older version of the CASTp results to Chimera in the past, but now a different newer set of results are available.  Chimera will check to see if you already fetched a specific CASTp result and it will just reopen that older one, unless in the Fetch by ID dialog you check the option to "Ignore any cached data."  So you could try that and see if it resolves the difference.  If not, my only ideas are those mentioned above.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/fetch.html>

So I can't tell you the exact answer of why you see a difference, only clarify that Chimera doesn't do the CASTp calculations, it just gets them from their website. Best regards,
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 Jun 9, 2014, at 10:37 AM, Felipe Vasquez <anfelvas at gmail.com> wrote:

> Hi,
> I am currently trying to identify certain features from a particular binding cavity, and  I decided to use CASTp plugin from Chimera. However, I realized that the data obtained directly from CASTp online server are not the same that those obtained by CASTp from Chimera. Examples include not only the number of pockets, but also the volume and surface area of them. What is the meaning of this confusing results?
> Thanks in advance for your help.
> Best regards,




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