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

Eric Pettersen pett at cgl.ucsf.edu
Tue Oct 9 17:12:28 PDT 2012

Yes, by default Chimera will place hydrogens to optimize hydrogen bonds first and avoid clashes second.  You can have it only consider clash avoidance by checking "steric only" in the dialog or by providing "hb false" in the command version.


                        Eric Pettersen
                        UCSF Computer Graphics Lab

On Sep 28, 2012, at 9:53 AM, Elaine Meng wrote:

> 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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