Thanks Elaine for your reply. In a quick question, I am trying to load two dcd files in chimera. Both files are obtained from same simulation(1-50ps first one and 50 to 100ps second one). How can I add these two dcd files in chimera.. When I am using MD movie tool then it is showing two window, one for first part and other for second part. Is it possible to merge both dcd files in chimera. VMD can read multiple dcd files but I want to use chimera for clear H bond analysis. Thank you On Wed, Mar 24, 2010 at 12:53 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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