<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Jan 7, 2013, at 2:53 AM, edu troche wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi chimera users, I was wondering if there is any way to build an average pdb from an Amber MD simulation of a system that doesn't contain any biopolymer. I know there is a script within the Amber suite, to generate an average pdb, but I'm doing the MD in several parts, and then reimaging them, so I wanted to check if the results of the Amber script, that makes an average on the coordinate file (.rst) without centering the system, is the same that I could have after applying the reimaging-centering script.</blockquote><br></div><div>Hi Eduardo,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>There is, sort of, but you have to modify your copy of Chimera -- though the modification isn't difficult. In the file <your Chimera>/share/Movie/average.py there are two calls to the "anaysisAtoms" function (on lines 22 and 47). If in both those calls you change "polymericOnly=True" to "polymericOnly=False" then you should be able to do the averaging you want.</div><div><br></div><div>--Eric</div><div><br></div><div>
<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; "><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><div><br></div><br class="Apple-interchange-newline"></span>
</div><div>P.S. On a mac, "<your Chimera>" will be "Chimera.app/Contents/Resources". Let me know if you need more info than that...</div>
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