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Re: [modeller_usage] Mutations



Hi,
I tried the example in http://salilab.org/modeller/wiki/Mutate_model, but my
model hasn't chains.
It has been calculated with Modeller and the residue that I would like to
change is the 27:

ATOM    203  N   ASP    27      16.536   9.555  15.986  1.00 91.26       1SG
204
ATOM    204  CA  ASP    27      16.891  10.947  16.025  1.00 91.26       1SG
205
ATOM    205  CB  ASP    27      18.072  11.218  16.974  1.00 91.26       1SG
206
ATOM    206  CG  ASP    27      18.307  12.718  17.052  1.00 91.26       1SG
207
ATOM    207  OD1 ASP    27      17.470  13.485  16.504  1.00 91.26       1SG
208
ATOM    208  OD2 ASP    27      19.335  13.117  17.662  1.00 91.26       1SG
209
ATOM    209  C   ASP    27      17.319  11.354  14.653  1.00 91.26       1SG
210
ATOM    210  O   ASP    27      17.069  12.473  14.212  1.00 91.26       1SG
211

However I tried to change the following parts in the script:

>#first argument
>modelname, respos, restyp, chain, = sys.argv[1:] 
I put: 
modelname, respos, restyp, = sys.argv[1:] 

>s = selection(mdl1.chains[chain].residues[respos])
I put 
s = selection(mdl1.residues[respos])

>s = selection(mdl1.chains[chain].residues[respos])
s = selection(mdl1.residues[respos])

But I have obtained a model very similar as that in input.
Should I try to change some parameter in the script?
Thank you in advance.
Laura

	--------- Original Message --------
	Da: Modeller Caretaker <>
	To: 
	        Cc: 
	Oggetto: Re: [modeller_usage] Mutations
	Data: 25/09/07 19:46
	
	> 
> 
> 
>  wrote:
> > I'm a new user of Modeller and I have a question about the model
computing.
> > If I take one/or more models with a given alignment and I change just
one or
> > more amino acids maintaning the same alignment, should I obtain a
different
> > model?
> > In other words, Can Modeller be used for calculating mutations?
> 
> Certainly - there has been some work done for SNPs using Modeller; see 
> http://salilab.org/modeller/wiki/Mutate_model for an example script.
> 
> 	Ben Webb, Modeller Caretaker
> -- 
>              http://www.salilab.org/modeller/
> Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
> 
> 
>  
 --
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