Hello,
I have been modelling GPCRs using multiple templates and have noticed that in the code below in my salign.py file:
aln = alignment(env) for (code, chain) in (('1', 'A'), ('2', 'A'), ('3', 'A')): mdl = model(env, file=code, model_segment=('FIRST:'+chain, 'LAST:'+chain)) aln.append_model(mdl, atom_files=code, align_codes=code+chain)
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? If this is the case, how can I determine which order of my templates is optimal for homology modelling? Thanks in advance,
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
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 >
On 09/24/2013 02:14 PM, HIDDEN wrote: > These different restraints due to the order of my templates do seem to > affect my side chain modelling.
Right, that's what I said.
> 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
Yes, this will happen. I'm not sure what you want me to say other than to simply repeat myself: you need to build multiple models.
Ben Webb, Modeller Caretaker
So how to I pick the "best" model from these multiple models. I assume these multiple models are produced from the differential order of my templates. On Tue, Sep 24, 2013 at 5:16 PM, Modeller Caretaker < modeller-care@salilab.org> wrote:
> On 09/24/2013 02:14 PM, HIDDEN wrote: > >> These different restraints due to the order of my templates do seem to >> affect my side chain modelling. >> > > Right, that's what I said. > > > 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 >> > > Yes, this will happen. I'm not sure what you want me to say other than to > simply repeat myself: you need to build multiple models. > > > 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 >
participants (2)
-
HIDDEN -
Modeller Caretaker