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@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