<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Jian,<div><span class="Apple-tab-span" style="white-space:pre"> </span>In addition there is a previous post on the chimera-dev list that is specifically germane to your request:</div><div><br></div><div><a href="http://www.cgl.ucsf.edu/pipermail/chimera-dev/2009/000634.html">http://www.cgl.ucsf.edu/pipermail/chimera-dev/2009/000634.html</a></div><div><br></div><div>Let me know if the info in that isn't enough for what you want to do.</div><div><br></div><div>--Eric<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 Oct 21, 2009, at 10:07 AM, Elaine Meng wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Jian,<br>There is no "dock prep" command, but there are commands "addh" and "addcharge":<br><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html</a>><br><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html</a>><br><br>Some other parts of Dock Prep can also be done with commands (for example "delete solvent"), but python scripting may be required for certain steps if you need them. I cannot advise on the python part, perhaps others can.<br><br>For scripting to handle multiple structures, please see previous posts such as:<br><<a href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003261.html">http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003261.html</a>><br><<a href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003262.html">http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003262.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 Oct 20, 2009, at 5:51 PM, Bisn wrote:<br><br><blockquote type="cite">Hello,<br></blockquote><blockquote type="cite">We are Chimera users trying to process 1000 proteins, e.g., add<br></blockquote><blockquote type="cite">hydrogen and charge. We want to do this via a Chimera for DOCK<br></blockquote><blockquote type="cite">preparation.<br></blockquote><blockquote type="cite">I know that Chimera accepts command line, but this is not realizable<br></blockquote><blockquote type="cite">for processing 10000 molecules. Have you any idea of the task?<br></blockquote><blockquote type="cite">Thanks!<br></blockquote><blockquote type="cite">Jian Chen</blockquote></div></blockquote></div></div></body></html>