[Chimera-users] opening CASTp results
pett at cgl.ucsf.edu
Wed Aug 13 17:33:06 PDT 2008
Starting with the daily build available tomorrow, Chimera will be
able to open your local CASTp results. You use the File->Open dialog
and select your pocket-atoms file (the ".poc" file). The other 4
files need to be in the same folder.
UCSF Computer Graphics Lab
On Jul 24, 2008, at 11:22 AM, Walter Novak wrote:
> Hi Elaine,
> I found a quick and easy workaround, but it involves editing the CASTp
> gui.py file and making a couple changes to the processCastpID
> function. Don't worry I duplicated this file first! I simply change
> basURL to include the directory and the root filename of my castp
> files, commented out the import (which is unnecessary), and altered
> the try statement to only attach the suffix to the name. Then I can
> use the fetch command and give it any bogus name to look for, like
> test, and it opens the files with the wonderful CASTp gui interface so
> I can select the channels. I have to change the baseURL for each new
> structure as I wasn't sure where it gets the castpID from, but that
> isn't so bad.
> def processCastpID(castpID):
> castpID = castpID.strip()
> if len(castpID) > 4:
> dir = "sccast"
> dir = "cast"
> castpID = castpID[:4].lower() + castpID[4:]
> baseUrl = "/Users/wnovak/Documents/NHpaper/ppNHase-het2-castp/
> #from urllib2 import urlopen
> pdb = baseUrl + ".pdb"
> mouthAtoms = baseUrl + ".mouth"
> mouthInfo = baseUrl + ".mouthInfo"
> pocketAtoms = baseUrl + ".poc"
> pocketInfo = baseUrl + ".pocInfo"
> raise UserError("ID %s not in CASTp database" %
> from CASTp import processCastpFiles
> structure, cavities = processCastpFiles(pdb, mouthAtoms,
> pocketAtoms, pocketInfo,
> CastpDialog(castpID, cavities)
> return [structure]
> On Jul 24, 2008, at 11:27 AM, Elaine Meng wrote:
>> Hi Wally,
>> Currently it is only possible to fetch data that is already in the
>> CASTp database, not data from using the CASTp server on your own
>> structure. They only provide such results as e-mail to the user.
>> We were thinking in the future we could add the ability to generate
>> the same convenient interface in Chimera when the user specifies the
>> name/location of the results files (that were mailed to him), but it
>> hasn't been done yet - sorry!
>> The results come in several separate files, so it is a little more
>> complicated than adding a new file type, but we believe it is doable.
>> Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
>> UCSF Computer Graphics Lab and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> On Jul 24, 2008, at 6:49 AM, Walter Novak wrote:
>>> Hi all,
>>> How can I open my own CASTp results easily? The fetch command works
>>> great, but I need to submit some modified structures, and I don't
>>> CASTp under file type in the open window.
>>> Walter R.P. Novak, Ph.D.
>>> Postdoctoral Fellow
>>> Rosenstiel Basic Medical Research Center
>>> Brandeis University
>>> 415 South St. MS 029
>>> Waltham, MA 02454-9110
>>> Phone: (781) 736-4944
>>> Fax: (781) 736-2405
> Walter R.P. Novak, Ph.D.
> Postdoctoral Fellow
> Rosenstiel Basic Medical Research Center
> Brandeis University
> 415 South St. MS 029
> Waltham, MA 02454-9110
> Phone: (781) 736-4944
> Fax: (781) 736-2405
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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