[Chimera-users] opening CASTp results

[Eric Pettersen]

Hi Wally,
	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.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu

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]
>
>
> 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
>
>
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080813/942dbff0/attachment.html>