[Chimera-users] Met CH3 and NH3+ hydrogen optimization

Elaine Meng meng at cgl.ucsf.edu
Fri Sep 28 09:53:26 PDT 2012

Dear Vis Kairys,
AddH does try to avoid clashes where possible.  It may be that your specific structure had other constraints, or that you ran into limitations of the clash-avoidance algorithm.

Besides rotating manually, other approaches include:

(a) energy minimization (you can freeze parts of the structure, for example to allow only hydrogens to move)

(b) adding hydrogens instead with the Richardson program "Reduce" (see the bottom of the AddH manual page linked above).

Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 28, 2012, at 12:34 AM, Visvaldas K. wrote:

> Dear colleagues,
> Regarding H addition to protein structures, there are indications that hydrogens of NH3+ groups of lysine or N-termini, and side chain methyls of methionines need a rotational optimization (Richardson & Richardson, Chapter 15 in "Structural Bioinformatics", 2nd ed., 2009, p. 380) . I think this problem is not too common, but I did encounter it at least once when I had to rotate manually a Methionine methyl to remove a clash with the ligand.  I think Chimera doesn't perform this optimization, or does it? If it doesn't, perhaps this could be put on a list of future improvements:)
> Best regards,
> Vis Kairys
> Institute of Biotechnology
> Vilnius University

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