November 2006 - modeller_usage

cyclic peptide modeling
by Giacomo Bastianelli 16 Nov '06

16 Nov '06

Dear users, I am modelling mutations and insertions of an original cyclic peptide sequence. However, when I run the modeling, I always loose my cyclization. Does modeller recognize cyclic peptides for the modeling? Thanks in advance, Giacomo Bastianelli

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question
by Widjaja, Linda 15 Nov '06

15 Nov '06

I am new to modeler. How do I convert my target sequence to PIR format?

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Hole in models
by hori koshii 13 Nov '06

13 Nov '06

(sorry this is a repeated question but it was missed and there was no answer to this) Hi everybody. I am wondering if anyone has got holes in many of the homology models generated? Any ways to control this? Thanks for answering. Good day. Sincerely, (P.S> the pdb was attached, you may select the "resid 165 to 185" and view as SURF on vmd, and you may see the hole I was referring to, thanks) --------------------------------- Cheap Talk? Check out Yahoo! Messenger's low PC-to-Phone call rates.

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Incorporation of hetero atom
by 서주현 13 Nov '06

13 Nov '06

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Re: [modeller_usage] How to use model.patch_ss_templates() ?
by Modeller Caretaker 08 Nov '06

08 Nov '06

jitrayut jitonnom wrote: > I am new for this program and i doubt on how to use > model.patch_ss_templates() in order to model disulfide bond of our model > from templates. As i read the FAQ no. 3, i am stil not understand that > where *_patch_disulfides.py_* be used. Since I know from the advanced > tutorials that there are many steps to run multiple template such as > salign.py , align2d_mult.py, model_mult.py, and evaluate_model.py. So, > which steps should be insertedt the patch_disulfides.py ? salign.py and align2d_mult.py are for alignment, and evaluate_model.py is for model evaluation. In all of these cases the definition of disulfide bonds is not required. model.patch_ss_templates() adds disulfide bonds in the model, if it is aligned with a template which has a disulfide. This is called automatically for you for 'automodel' so you don't generally need to worry about it. An example is given in FAQ #3 of how to add specific disulfide bonds in the 'automodel' procedure, using model.patch(). This only applies to the model building step, of course - model_mult.py in your case. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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Hole in models
by hori koshii 02 Nov '06

02 Nov '06

Hi everybody. I am wondering if anyone has got holes in many of the homology models generated? Any ways to control this? Thanks for answering. Good day. Sincerely, --------------------------------- Check out the New Yahoo! Mail - Fire up a more powerful email and get things done faster.

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