[Chimera-users] opening CASTp results
meng at cgl.ucsf.edu
Thu Jul 24 11:33:48 PDT 2008
Wow, I'm impressed!! It takes a brave person to mess around with
Chimera code. 8-) Thanks for sharing your solution, which many
others may find useful until we provide an interface for opening local
CASTp results. Best,
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]
> 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
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