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.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html>

Besides rotating manually, other approaches include:

(a) energy minimization (you can freeze parts of the structure, for example to allow only hydrogens to move)
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html>

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

Best,
Elaine
-----
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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