[chimera-dev] Help with "looping through PDB IDs" script

Navya Shilpa Josyula njosyu2 at uic.edu
Mon Apr 21 17:04:24 PDT 2014

Hi Elaine and Eric,

Thank you for your replies. As per your suggestions, I tried using the
processCastpFIles functions, but I was not able to figure out using thee
functions. So I downloaded the files manually from CASTp server. However
for ASA and Bfactor values, with your help I was able to get those values
from chimera for all of my 400 proteins.

I really appreciate you for helping me on this.

Thanks a lot,

On Mon, Apr 21, 2014 at 4:46 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Navya,
> As per Elaine's remarks, Chimera has no capability to upload a file to
> CASTp and process the results.  processCastpID() gets the files for
> *standard* PDB IDs and uses processCastpFiles() to process them.
>  processCastpFiles() could be called by itself, but you would have had to
> obtain the files by using the CASTp web server yourself -- obviously not a
> great solution for you.
>  If CASTp had offered a REST interface to its web server I would have
> probably implemented built-in upload, but with email notification as the
> only option it was just way too ugly and difficult.
>  I don't know that there are any good options here, other than possibly
> using the standard PDB entries if that is compatible with the other aims of
> your research.
> --Eric
> On Apr 21, 2014, at 10:07 AM, Elaine Meng <meng at cgl.ucsf.EDU> wrote:
> Hi Navya,
> I'm not sure if this is your question, but it is not possible to submit
> structures from Chimera to the CASTp web server for a new calculation.  The
> only way to run a new calculation is by submitting directly at their
> website.
> <http://sts-fw.bioengr.uic.edu/castp/calculation.php>
> The CASTp fetch from Chimera is only getting pre-calculated results for
> existing PDB entries from the CASTp database.
> I hope this clarifies the situation,
> 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 17, 2014, at 10:12 PM, Navya Shilpa Josyula <njosyu2 at uic.edu>
> wrote:
> Hi Eric,
> Thank you for your reply. I am understanding that the castp python script
> works only for .pdb files. But it would be really time consuming for me to
> upload each of the .pdb1 file to castp and then download the .poc and
> .pocInfo files as I have to process these two files again to extract the
> atoms list, pocID and MS_volume values.
> Could you please elaborate more on how to extract the .poc and .pocInfo
> values for .pdb1 files from CASTp server using processCastpID() and
> processCastpFiles(). I need to be able to loop through all .pdb1 files and
> for each pdb1 file I need to get the atoms list for each pocID along with
> pocVolumes and to write these values into a .csv file.
> Thank you in advance,
> Navya
> On Thu, Apr 17, 2014 at 5:05 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> On Apr 17, 2014, at 2:11 PM, Navya Shilpa Josyula <njosyu2 at uic.edu> wrote:
> Now I am trying to write CASTp information for each of my proteins into a
> separate file. As you suggested in earlier email, the processCastpID
> function is in the gui.py file but not in __init__.py file. Hope I am not
> missing anything here. As per my understanding, this function is fetching
> the 4 castp files of which I would require only ".poc" and ".pocInfo"
> files. From these two files I want to write the data of only atoms list,
> pocID and MS_Volume data into a single file for all 400 proteins in my
> dataset. Is there a link or any script available for such requirement?
> There are some fine points that I missed in my answer yesterday, and the
> situation is complicated further by your use of .pdb1 files instead of the
> "normal" entries.
> So for one thing, if you are going to use the .pdb1 files, then you are
> going to have to run CASTp yourself on each and then process the results.
>  In that case you might as well also analyze the .poc and .pocInfo files
> yourself to determine what pocket each atom belongs to (the next-to-last
> field in the .poc file) and the volume of that pocket (listed in the
> .pocInfo file).
> The main point I missed in my reply, which may now be moot because of the
> .pdb1 thing, is that processCastpID() builds its own structure and
> therefore you would not open the PDB first, you would instead return the
> structure (along with the cavities list) from that method and make the
> structure available in chimera with:
> chimera.openModels.add([structure])
> and then proceed with selecting the right residues, using
> currentResidues() to list them, etc.  I guess if you didn't want to process
> the .pdb1 CASTp files yourself (after running CASTp on the .pdb1) you could
> use processCastpFiles() to get the cavity list and structure and proceed as
> I just outlined.  processCastpFiles is in __init__, unlike processCastpID()
> as you found!
> Again, as mentioned in my last email, since my output files will be huge
> in size, will I be able to write my files directly to a database table in
> SQL server?
> I'm not much of an expert on this, but maybe this page would help:
> DatabaseInterfaces - Python Wiki
> --Eric
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