Thank you very much Elaine. It is working fine now. I was using wrong command from chimera import runCommand for HbonDNum in range(1, 1000): runCommand("hbonds saveFile ligand.%03d.hbonds" % HbonDNum) On Fri, Jan 29, 2010 at 1:08 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi S, If you wanted only how many H-bonds there are at each step sent to a file, you can just save the contents of the Reply Log (under Favorites menu). You would define the script in MD Movie, then clear the Reply Log, then run the trajectory through from start to end one time (with Loop turned off). Then click Save on the Reply Log to save its contents to a text file.
If you wanted the detailed results of which atoms are H-bonding and their distances at each step, it can be done with the "saveFile" option of the "findhbond" command. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findhbond.html>
The MD Movie per-frame script capability allows inserting the frame number in the filename so you can get a different H-bond results file for each step. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>
For example, the per-frame script could have something like
findhbond saveFile ~/Desktop/hbondinfo-<FRAME>.txt
(plus any other options of that command you might want) which puts all the information from frame 1 into hbondinfo-001.txt, frame 2 hbondinfo-002.txt, ... files on my mac Desktop.
Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Jan 29, 2010, at 10:02 AM, snoze pa wrote:
I checked the results with molmol and it seems chimera results are correct. I want to save the number of hbonds in each frame. When I use the command hbond in chimera script movie menu command then it prints correct number of hbonds in every frame. Can you help me how to save the results from each frame(total no of hbonds). thank you S
On Thu, Jan 28, 2010 at 4:59 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
I forgot to mention: from looking at the images, I would say the Chimera results are more reasonable, because that's how beta-sheets form, with strand-strand hydrogen bonds. In the VMD view, some strands lack H-bonds to the next strand in the sheet, or only have one.
Of course, these statements are only qualitative, but it was my first impression. Elaine
On Jan 28, 2010, at 2:36 PM, snoze pa wrote:
Hi Elaine, Thanks for your help. But somehow I am getting different number of bonds in vmd and chimera. A snap shot of the figure is shown below.
http://img191.imageshack.us/img191/9084/screenshotva.png
In VMD the Hbonds are calculated by show Hbonds and protein. Vms shows 24 hbonds while chimera shows 38 hbonds. I don't know how to justify this. I will highly appreciate your help. A snapshot is shown in the link http://img191.imageshack.us/img191/9084/screenshotva.png
Thanks s
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