<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Chinh,<div><span class="Apple-tab-span" style="white-space:pre"> </span>If you are able to write a Python script, you could use the info in the Chimera Programmer's Guide</div><div><br></div><div><a href="http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide">http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide</a></div><div><br></div><div>to write a script to get the values. There is a programmer's example specifically about atomic-level measurements such as angles and distances:</div><div><br></div><div><a href="http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/Main_AtomMeasure.html">http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/Main_AtomMeasure.html</a></div><div><br></div><div>Also, Python is reasonably easy to learn, especially if you already know how to program in another language. There are links to Python tutorials in the Programmer's Guide.</div><div><br></div><div>--Eric</div><div><br><div><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 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; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> 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: normal normal normal 16px/normal Helvetica; "> 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: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div><br class="Apple-interchange-newline"></span></div><div><div>On Mar 8, 2013, at 9:08 AM, Elaine Meng wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Chinh,<br>For scripting measurements (distance, angle, torsion) you can use commands: distance, angle<br><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html</a>><br><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html</a>><br><br>These measurements are specified individually. Chimera does not have an option to write out a Z-matrix, sorry.<br><br>More info on writing Chimera scripts to process multiple data files:<br><<a href="http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html">http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html</a>><br><br>I hope this helps,<br>Elaine<br>-----<br>Elaine C. Meng, Ph.D. <br>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>Department of Pharmaceutical Chemistry<br>University of California, San Francisco<br><br>On Mar 8, 2013, at 12:01 AM, Chinh Su Tran To wrote:<br><br><blockquote type="cite">Hi,<br></blockquote><blockquote type="cite">I have some results after running docking from DOCK.<br></blockquote><blockquote type="cite">I'd like to obtain information of internal coordinates (bond, angle, torsion OR z-matrix).<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Could anyone please give me any suggestion how to do that in Chimera? Or if possible, please suggest me some references that can help me find it out.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I have bunch of conformations, so I may not use the gui. <br></blockquote><blockquote type="cite">Thank you.<br></blockquote><blockquote type="cite">Chinh<br></blockquote><br><br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></div></blockquote></div><br></div><br></body></html>