[Chimera-users] average pdb

Eric Pettersen pett at cgl.ucsf.edu
Mon Jan 7 14:11:35 PST 2013

On Jan 7, 2013, at 2:53 AM, edu troche wrote:

> 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.

Hi Eduardo,
	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.


                        Eric Pettersen
                        UCSF Computer Graphics Lab

P.S.  On a mac, "<your Chimera>" will be "Chimera.app/Contents/Resources".  Let me know if you need more info than that...

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