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