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 modeller-care@salilab.org To: Cc: modeller_usage@salilab.org Oggetto: Re: [modeller_usage] Mutations Data: 25/09/07 19:46 > > > > laura.buttazzo@email.it 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 > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > -- Email.it, the professional e-mail, gratis per te: http://www.email.it/f
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