[Chimera-users] opening CASTp results

[Walter Novak]

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]


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.
> Best,
> Elaine
> -----
> 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
>                     http://www.cgl.ucsf.edu/home/meng/index.html
>
> 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 see
>> CASTp under file type in the open window.
>> Thanks,
>> Wally
>>
>> 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