Hi Si,
Something that may help is using a statistical torsion angle potential term.
Although no substitute for experimental restraints, it will at least help
getting rid of rotamer outliers, so that you are left with plausible ones.
(Note that, in the standard approach, this term applies to all the residues. It
also affects the backbone, improving the Ramachandran statistics.)
You can access the latest version of this potential, called "torsionDBPot"
[Bermejo et. al. (2012) Protein Sci. 21: 1824], through the Python interface.
For an example on how to set it up you can take a look at
xplor/eginput/gb1_rdc/refine.py, where "xplor" refers to your Xplor-NIH
directory.
Additionally, you may want to explore TALOS-N, which now predicts chi1 torsion
angles.
I hope it helps.
Best,
Guillermo
________________________________________
From: Si Yan [s...@udel.edu]
Sent: Wednesday, April 09, 2014 5:06 PM
To: xplor-...@nmr.cit.nih.gov
Subject: [Xplor-nih] A question about rotamers
Hello Charles and others,
I have refined some structures from solid-state NMR restraints. When we
compare the NMR structure of our protein with X-ray structures with different
binding partners, we find some PHE's aromatic rings present rotamer difference
between NMR structure and the X-ray structures. It is hard for us to judge that
this rotamer difference is a result of real difference in structures or it is
just because of lacking of restraints to constrain the side-chain torsion
angles.
We only used distance restraints and backbone torsion angle restraints for
the structure refinements. In our NMR restraints list for the structure
refinement, there is no restraints from the atoms of the aromatic rings.
My question is there any way to constrain the side-chain torsion angle in
Xplor-NIH?
I saw a function named correctSymmetricSidechains in selectTools module.
But I am not sure if this the correct thing I should include in my refinements.
If this is what I could use, how can I use it properly?
Thanks very much!
Best
Si
--
Si Yan
Department of Chemistry and Biochemistry
University of Delaware
Newark, DE, 19716
Email to s...@udel.edu<mailto:s...@udel.edu>
Phone: 302-831-8624
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