<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Feb 24, 2010, at 5:34 PM, Yang wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Eric<br><br>I want to manipulate with electron density maps, and just use chimera functions for reading pdb files and density maps. However, for high-resolution maps, it takes too long to run the my program on my mac book. So I want to remotely use the server of our department, which has much larger memory, to complete this task by typing commands in terminal. Before that, I had everything done in chimera's IDLE. So I prefer using chimera functions somehow in terminal assuming chimera is installed first.<br><br>Thanks for your advice.</div></blockquote><br></div><div>I think you just want to take whatever commands you were using in IDLE and put them in a Python script (file ending: .py). You can then execute them with "chimera --nogui myscript.py". If you need to supply arguments to the script then instead run it like this: "chimera --nogui --script myscript.py -- arg1 arg2 ...". This is described here:</div><div><br></div><div><a href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/options.html">http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/options.html</a></div><div><br></div><div>--Eric</div><br><div><span class="Apple-style-span" style="font-size: 16px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><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"></div></span></div></body></html>