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

Thanks Elaine, I highly appreciate your time and help. Meanwhile I am use catdcd to cat multiple dcd files into chimera. I will download the latest build to check it. On Wed, Mar 24, 2010 at 6:07 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:

On Mar 24, 2010, at 1:23 PM, snoze pa wrote:

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

Hi S, There is support for multiple Amber trajectory files, but not DCDs.  So I took the multi-file Amber code and with some pushing and pulling added it to the DCD file code.  So in tomorrow's build you will be able specify multiple DCD files initially, or add additional DCD files with the Movie interface's File...Add Additional Frames menu entry. --Eric

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        http://www.cgl.ucsf.edu