<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">I guess I should have mentioned that you would run the Python script by opening it in Chimera, either with File..Open or with the "open" command. The script should have a ".py" suffix in order for Chimera to recognize it as a Python script.<div><br></div><div>--Eric</div><div><br><div><div>On Jul 27, 2009, at 1:48 PM, Eric Pettersen wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Anna,<div><span class="Apple-tab-span" style="white-space:pre"> </span>One possibility if you know shell scripting is to use PROCHECK (<a href="http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html">http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html</a>) on your PDB files.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Otherwise it depends on whether you know Python scripting or a programming language of any kind. If you know a non-Python programming language you would use that language to generate a script that does the following for your 10000 files:</div><div><br></div><div>open blah1.pdb</div><div>findclash :LIG saveFile out1.txt</div><div>close all</div><div>...repeat for file 2, 3, etc.</div><div><br></div><div>where LIG is the residue type of your ligand. If the residue type varies for each file then using 'ligand' instead of ':LIG' might be sufficient.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>If you know Python you can do it somewhat more directly with a script with an embedded loop, something along the lines of:</div><div><br></div><div>import os</div><div>from chimera import runCommand as rc</div><div>rc("cd /dir_with_pdb_files")</div><div>for fname in os.listdir("."):</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>if not fname.endswith(".pdb"):</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>continue</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>rc("open " + fname)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>rc("findclash :LIG saveFile " + fname[:-4] + ".out")</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>rc("close all")</div><div><br></div><div>which basically does the same functions as the first script file but uses a loop instead of writing out all 10000 iterations explicitly.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Let me know if you have more questions.</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; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 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></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 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></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 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></div><br class="Apple-interchange-newline"></div></span> </div><br><div><div>On Jul 27, 2009, at 1:30 AM, Anna Feldman-Salit wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear Users and Developers,<br><br>I'm interested in using a FindClashes option for a large set of files. <br>It is about finding clashes between a small ligand and enzyme which are <br>found at different conformational stages (more than 10000 each).<br><br>How can one do it iteratively? I understand this is a scripting or could <br>it be that such an application already exists?<br><br>Thanks in advance.<br><br>Regards,<br><br>Anna<br><br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br><a href="http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br></div></blockquote></div><br></div></div>_______________________________________________<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></blockquote></div><br></div></body></html>