Re: [modeller_usage] A single type of rotamer

[Thomas Evangelidis <>]

You probably need to tune Modeller to set all lysine rotamers to the the straight conformation on the fly, otherwise you may get biased models -especially if the Lys residues are buried within the protein. If this isn't the case and you just want to adjust a few side-chains on the surface then you can use Chimera (read section "Angles, Rotamers and Clashes" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/frametut.html). With Chimera you can correct interactively every residue you like and also see what steric clashes or H-bonds are formed by every rotamer. I use it a lot to improve my models or adjust side-chains in the active site.

Otherwise you will need a more drastic solution (not sure if possible), namely tuning Modeller to do that directly. Modeller Caretaker is the designated person to answer that question.

best,
Thomas

On 10 October 2010 22:39, James Irving <">> wrote:

Hi Omar,

Presumably if you know the rotamer the lysine adopts it is from a solved crystal structure, with good B-factors for the atoms?  Anyway, Coot is a crystallographic model building program that lets you play with rotamers (http://www.biop.ox.ac.uk/coot/).

Cheers,
James

On 9 October 2010 05:38, Omar Piña <" target="_blank">> wrote:

Hi,

I need to model a protein with the lysine all straight (stuck-up?). How can I say to modeller that only create models with the lysine in that form?? This Lysine is known to be like that. Thanks!!

Omar

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