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. Thank you! -- Eduardo Troche Pesqueira <http://webs.uvigo.es/webqo3/people/eduardo.html> Tel. 986812309 Edificio E, Andar 3º, Laboratorio1 Facultade de Químicas Departamenteo de Química Orgánica Lagoas-Marcosende Universidade de Vigo
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 Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu 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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edu troche -
Eric Pettersen