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 ----- 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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users