Re: [modeller_usage] modelling with multiple templates
To: Modeller Caretaker <>
Subject: Re: [modeller_usage] modelling with multiple templates
From: HIDDEN <HIDDEN>
Date: Tue, 24 Sep 2013 17:14:59 -0400
Cc:
Dear Modeller Caretaker,
These different restraints due to the order of my templates do seem to affect my side chain modelling. Essentially what I've been doing is create 5 different models, select the one with the lowest DOPE score, and let SCRWL4 add in the side chains. When I switch the order of my templates in salign.py, and do the whole procedure again, I get a model where the side chains are positioned differenty, and consequently some polar contacts are lost. Please advise,
HIDDEN
On Mon, Sep 23, 2013 at 4:08 PM, Modeller Caretaker <" target="_blank">> wrote:
On 09/15/2013 02:57 PM, HIDDEN wrote:
if I switched the order of the templates to be 3, 1, 2 instead of the order shown above (1,2,3), I get different models with different DOPE
scores. Is this possible or am I doing something wrong?
Sure, that will happen, since the restraints will be slightly different. The models should still be selected from the same ensemble though (so if you build multiple models, any differences should average out). Don't waste time trying to find an "optimal order" for the templates.