[Chimera-users] opening CASTp results

[Elaine Meng]

Hi Wally,
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,
Elaine

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.
> Best,
> Wally
>
> def processCastpID(castpID):
>        castpID = castpID.strip()
>        if len(castpID) > 4:
>                dir = "sccast"
>        else:
>                dir = "cast"
>        castpID = castpID[:4].lower() + castpID[4:]
>        baseUrl = "/Users/wnovak/Documents/NHpaper/ppNHase-het2-castp/ 
> JIDF34763I670"
>
>        #from urllib2 import urlopen
>        try:
>                pdb = baseUrl + ".pdb"
>                mouthAtoms = baseUrl + ".mouth"
>                mouthInfo = baseUrl + ".mouthInfo"
>                pocketAtoms = baseUrl + ".poc"
>                pocketInfo = baseUrl + ".pocInfo"
>        except:
>                raise UserError("ID %s not in CASTp database" %  
> castpID)
>
>        from CASTp import processCastpFiles
>        structure, cavities = processCastpFiles(pdb, mouthAtoms,  
> mouthInfo,
>                                pocketAtoms, pocketInfo,  
> identifyAs=castpID)
>        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
>
>
>
>