Dear all,<div><br></div><div>Thank you very much for your help. I am coding it in python and will run in batch mode.</div><div>I think it will work.</div><div><br></div><div>Chinh<br><br><div class="gmail_quote">On Sat, Mar 9, 2013 at 2:01 AM, Eric Pettersen <span dir="ltr"><<a href="mailto:pett@cgl.ucsf.edu" target="_blank">pett@cgl.ucsf.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Chinh,<div><span style="white-space:pre-wrap"> </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" target="_blank">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" target="_blank">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 style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:16px;white-space:normal;font-family:Helvetica;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" target="_blank">http://www.cgl.ucsf.edu</a></font></div>
<br></span></div><div><div><div class="h5"><div>On Mar 8, 2013, at 9:08 AM, Elaine Meng wrote:</div><br></div></div><blockquote type="cite"><div><div><div class="h5">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" target="_blank">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" target="_blank">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" target="_blank">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></div></div>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu" target="_blank">Chimera-users@cgl.ucsf.edu</a><br><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br>
</div></blockquote></div><br></div><br></div></blockquote></div><br></div>