<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Wally,<div><span class="Apple-tab-span" style="white-space:pre"> </span>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.</div><div><br></div><div>--Eric</div><div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p></div></span> </div><br><div><div>On Jul 24, 2008, at 11:22 AM, Walter Novak wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Elaine,<br><br>I found a quick and easy workaround, but it involves editing the CASTp <br>gui.py file and making a couple changes to the processCastpID <br>function. Don't worry I duplicated this file first! I simply change <br>basURL to include the directory and the root filename of my castp <br>files, commented out the import (which is unnecessary), and altered <br>the try statement to only attach the suffix to the name. Then I can <br>use the fetch command and give it any bogus name to look for, like <br>test, and it opens the files with the wonderful CASTp gui interface so <br>I can select the channels. I have to change the baseURL for each new <br>structure as I wasn't sure where it gets the castpID from, but that <br>isn't so bad.<br><br>Best,<br>Wally<br><br>def processCastpID(castpID):<br> castpID = castpID.strip()<br> if len(castpID) > 4:<br> dir = "sccast"<br> else:<br> dir = "cast"<br> castpID = castpID[:4].lower() + castpID[4:]<br> baseUrl = "/Users/wnovak/Documents/NHpaper/ppNHase-het2-castp/ <br>JIDF34763I670"<br><br> #from urllib2 import urlopen<br> try:<br> pdb = baseUrl + ".pdb"<br> mouthAtoms = baseUrl + ".mouth"<br> mouthInfo = baseUrl + ".mouthInfo"<br> pocketAtoms = baseUrl + ".poc"<br> pocketInfo = baseUrl + ".pocInfo"<br> except:<br> raise UserError("ID %s not in CASTp database" % <br>castpID)<br><br> from CASTp import processCastpFiles<br> structure, cavities = processCastpFiles(pdb, mouthAtoms, <br>mouthInfo,<br> pocketAtoms, pocketInfo, <br>identifyAs=castpID)<br> CastpDialog(castpID, cavities)<br> return [structure]<br><br><br>On Jul 24, 2008, at 11:27 AM, Elaine Meng wrote:<br><br><blockquote type="cite">Hi Wally,<br></blockquote><blockquote type="cite">Currently it is only possible to fetch data that is already in the <br></blockquote><blockquote type="cite">CASTp database, not data from using the CASTp server on your own <br></blockquote><blockquote type="cite">structure. They only provide such results as e-mail to the user. <br></blockquote><blockquote type="cite">We were thinking in the future we could add the ability to generate <br></blockquote><blockquote type="cite">the same convenient interface in Chimera when the user specifies the <br></blockquote><blockquote type="cite">name/location of the results files (that were mailed to him), but it <br></blockquote><blockquote type="cite">hasn't been done yet - sorry!<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">The results come in several separate files, so it is a little more <br></blockquote><blockquote type="cite">complicated than adding a new file type, but we believe it is doable.<br></blockquote><blockquote type="cite">Best,<br></blockquote><blockquote type="cite">Elaine<br></blockquote><blockquote type="cite">-----<br></blockquote><blockquote type="cite">Elaine C. Meng, Ph.D. <a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a><br></blockquote><blockquote type="cite">UCSF Computer Graphics Lab and Babbitt Lab<br></blockquote><blockquote type="cite">Department of Pharmaceutical Chemistry<br></blockquote><blockquote type="cite">University of California, San Francisco<br></blockquote><blockquote type="cite"> <a href="http://www.cgl.ucsf.edu/home/meng/index.html">http://www.cgl.ucsf.edu/home/meng/index.html</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On Jul 24, 2008, at 6:49 AM, Walter Novak wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Hi all,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">How can I open my own CASTp results easily? The fetch command works<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">great, but I need to submit some modified structures, and I don't see<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">CASTp under file type in the open window.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Thanks,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Wally<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Walter R.P. Novak, Ph.D.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Postdoctoral Fellow<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Rosenstiel Basic Medical Research Center<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Brandeis University<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">415 South St. MS 029<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Waltham, MA 02454-9110<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Phone: (781) 736-4944<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Fax: (781) 736-2405<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><br><br>Walter R.P. Novak, Ph.D.<br>Postdoctoral Fellow<br>Rosenstiel Basic Medical Research Center<br>Brandeis University<br>415 South St. MS 029<br>Waltham, MA 02454-9110<br>Phone: (781) 736-4944<br>Fax: (781) 736-2405<br><br><br><br><br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></div></blockquote></div><br></div></body></html>