<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Chris,<div><span class="Apple-tab-span" style="white-space:pre"> </span>And if you feel you still need to use Python (for looping perhaps) then you should look at the <a href="http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html">Chimera Programmer's Guide</a>, particularly the examples and the FAQ.</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><br class="Apple-interchange-newline"></div></span> </div><br><div><div>On Apr 7, 2009, at 12:18 PM, Elaine Meng wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear Chris,<br>I can't answer about Python, but you may be able to do what you want <br>using Chimera command scripts. There is a rich set of commands, and <br>the same commands you would enter at the command line can be placed <br>in a text file. Simply opening that command file in Chimera will <br>execute all the commands.<br><br>Chimera command documentation for the current daily build:<br><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecommand.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecommand.html</a>><br><br>Example command files:<br><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/</a> <br>indexcommand.html#cmdfile><br><br>I hope this helps,<br>Elaine<br>-----<br>Elaine C. Meng, Ph.D. <a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a><br>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>Department of Pharmaceutical Chemistry<br>University of California, San Francisco<br> <a href="http://www.cgl.ucsf.edu/home/meng/index.html">http://www.cgl.ucsf.edu/home/meng/index.html</a><br><br><br>On Apr 7, 2009, at 11:11 AM, christopher lau wrote:<br><br><blockquote type="cite">Dear Madam/Sir<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I am new to Chimera and this forum so I apologize in advance if I <br></blockquote><blockquote type="cite">my question is inappropriate.<br></blockquote><blockquote type="cite">I want to start writing python scripts such that I can run the <br></blockquote><blockquote type="cite">script and the color code, orientation, etc of the molecule opened <br></blockquote><blockquote type="cite">can be automated. Do you know of any good tutorials that teach <br></blockquote><blockquote type="cite">what commands are available to use in python for chimera and how to <br></blockquote><blockquote type="cite">run some basic python scripts in chimera? I have figured out <br></blockquote><blockquote type="cite">enough to open the Python Shell in Chimera, but that is all. An <br></blockquote><blockquote type="cite">example python script would be helpful.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks everyone,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Chris Lau<br></blockquote><blockquote type="cite">_<br></blockquote>_______________________________________________<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>