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Re: [modeller_usage] Need Help with model accuracy

Mª Victoria Ruiz Pérez wrote:
> I´m a begginer user of MODELLER, and I have a question for you: 
> I´m making docking experiments, and the protein I have got from the PDB
> has some gaps, so the docking can´t go on. So, I thought I could model
> the protein using its own cristal as template. So I did,  but the models
> I got don´t fit very well with the original cristal (when I superimpose
> them with MacPyMol, the models are very deviated from the cristal). What
> can I do to improve the adjustment between models and template?

Modeller should produce models that look like the template where the two
are aligned, by construction. Presumably you have a 1:1 alignment in
this case, since you're modeling using its own sequence - the sequence
identity is 100% ? So in this case the models should look exactly like
the template, differing only in sidechain orientations. If not,
something is very wrong - you should check the restraint violations in
the log file, because the restraints cannot be satisfied.

	Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage