<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Supplementing Elaine’s answer, it is also possible to run Dock Prep in batch mode, but you have to resort to a Python script. See this message:<div class=""><br class=""></div><div class=""><a href="http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html" class="">http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html</a></div><div class=""><br class=""><div class=""><div class="">—Eric</div><div class=""><br class=""></div><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div></div>
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<br class=""><div><blockquote type="cite" class=""><div class="">On Nov 14, 2016, at 9:49 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Dear Aaran,<br class="">If you just want to convert the format (not do all the other Dock Prep stuff), you can use the “open” command to open the PDB file and the “write” command to save it as a Mol2 file. There are also commands to add hydrogens (addh) and charges (addcharge), but not for every part of Dock Prep. Once you have tried the commands and figured out how to use them, then you would probably want to put them into a Python script that will loop through a lot of files, see:<br class=""><br class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html" class="">http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html</a>><br class=""><br class="">See also the command manual pages for the options:<br class=""><br class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/open.html" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/open.html</a>><br class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html</a>><br class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html</a>><br class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html</a>><br class=""><br class="">However, if you only wanted to convert formats, it might be more efficient to use something else like Babel instead of Chimera.<br class=""><br class="">I hope this helps,<br class="">Elaine<br class="">----------<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><br class=""><blockquote type="cite" class="">On Nov 11, 2016, at 6:32 AM, <a href="mailto:wang_q@tib.cas.cn" class="">wang_q@tib.cas.cn</a> wrote:<br class=""><br class="">Dear Colleagues,<br class=""> I am a beginner in docking(using DOCK 6.7). I learned from DOCK6 tutorial that I could use UCSF chimera to prepare my inputs file for DOCK6 and I prepared the inputs mol2 format file ( converting from PDB to mol2) successfully indeed. And now I have a question, is there a way that I can use in commend line to convert PDB to mol2 format file in chimera, because I want to use this format conversion function in server. I would be very grateful if someone could help me solve the puzzle.<br class="">Thanks very much!<br class="">Aaran<br class=""></blockquote><br class=""><br class="">_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""><br class=""></div></div></blockquote></div><br class=""></div></div></body></html>