<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="">Hi Jose,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>All Elaine’s info is correct. In case your question was about using Chimera functions from your own Python interpreter, see this recent chimera-users thread:</div><div class=""><br class=""></div><div class=""><a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-September/012704.html" class="">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-September/012704.html</a></div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><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><br class="Apple-interchange-newline">
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<br class=""><div><blockquote type="cite" class=""><div class="">On Sep 14, 2016, at 11:02 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="">Hi Jose,<br class="">You can create an input test file that is a script with a series of instructions in either Chimera commands or Python, and then from the command line, start Chimera in nogui mode and specify that input file.<br class=""><br class="">Startup from system command line, see also - -nogui startup option:<br class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/startup.html" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/startup.html</a>><br class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/options.html" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/options.html</a>><br class=""><br class="">Input file types including Chimera command files and Python scripts:<br class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#command" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#command</a>><br class=""><br class="">Basic primer on Python scripting for Chimera:<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="">Some possible reasons to use Python instead of Chimera command scripts are if you need looping, or some function that is not available as a Chimera command.<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="">On Sep 10, 2016, at 6:45 PM, José Almeida <<a href="mailto:jose.gcp.almeida@gmail.com" class="">jose.gcp.almeida@gmail.com</a>> wrote:<br class=""><br class=""><blockquote type="cite" class="">Hello,<br class="">I am a beggining Chimera user and was wondering if it was possible to run, all in the same command, something that enabled me to use a function (e.g. hbonds) without utilizing the console or the gui. I am trying to include this into a program so that I can calculate H-Bond data on several proteins in order to automatize the procedure, but I haven't been able to do so.<br class=""><br class="">Already thanking any attention given to this problem,<br class="">Best regards,<br class="">José Guilherme de Almeida<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></body></html>