[Chimera-users] Question related to chimera H-bond constraints

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 24 10:53:48 PDT 2010

Dear S,
In both #1 and #2 you have checked "Relax" so you are using the  
relaxed values, and will get the same total (76).  The only difference  
is coloring: in #1 all 76 are colored cyan, whereas in #2 the ones  
meeting the strict criteria (50) are cyan and the ones that do not  
meet the strict criteria but do meet the relaxed criteria (26) are  
red.  In #3 you only have the strict ones.
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 24, 2010, at 10:21 AM, snoze pa wrote:

> Dear Chimera Users,
> I have a question related to number of hydrogen bonds.
> 1.  When I am using the Relax H-bond constraints then chimera is
> showing 76 H-bonds as shown below figure (h bonds are shown in cyan
> color)
> http://img260.imageshack.us/img260/6467/screenshotau.png
> 2. If I will select the option color H bonds not meeting precise
> criteria differently, then still it shows 76 H bonds with some bonds
> that do not meet the criteria in red color
> http://img690.imageshack.us/img690/5607/screenshot1ks.png
> In 2, Why the red H bonds are different from 1 though H bonds are
> relaxed. If it is true then why chimera is showing these bonds in
> Relax H-bond constraints in 1.
> 3. However, if I will not choose the option to relax H bonds
> constraints then it is showing 50 H bonds as shown below
> http://img153.imageshack.us/img153/3822/screenshot2kr.png
> Thank you very much for your time and help.
> S
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