Re: [modeller_usage] modeling different conformations of a protein from related structures

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 5/7/12 7:35 AM, EGY wrote:
> Sorry, my question is much more elementary.

Your original question was addressed just last week on the mailing list:
http://salilab.org/archives/modeller_usage/2012/msg00152.html

> I see an example from the tutorial (Advanced Modeling, Modeling
> ligands in the binding site) on an alignment similar to what I want.
> However, I don't see the associated script to give this alignment

You make the alignment yourself, e.g. in a text editor. There is no 
script to generate it for you automatically.

> In this example, only the binding pocket of the 1emd structure was
> included in the alignment. I would also need to know how not to
> include a region in one of the other sequences.

Either edit the PDB file to remove the region you don't want to include, 
or see http://salilab.org/modeller/9.10/FAQ.html#2

	Ben Webb, Modeller Caretaker
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