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,
On Mon, Sep 23, 2013 at 4:08 PM, Modeller Caretaker < modeller-care@salilab.org> 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. > > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/**modeller/http://www.salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/**listinfo/modeller_usagehttps://salilab.org/mailman/listinfo/modeller_usage >