Hi Bala, The distances all go to the Reply Log, you can save them from there. See also these previous posts: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-February/002379.html

<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-February/002378.html

(See link to python that can be used as a per-frame script at the bottom of that post. In that case you would just define the distance monitor(s) by hand one time before running the script. Again all of the info would go to the Reply Log, so it is basically similar to my Chimera per-frame script suggestion, except that you could modify the python to include frame number in the output lines.) 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 Dec 23, 2009, at 10:43 AM, Bala subramanian wrote:

Hi Elaine, Your idea works. But how can direct the output to a file rather than seeing it on the chimera window. I gave ~distance distance :163@CA :166@CA and then tried savefile option but nothing is saved in the output file except the two lines of command. Could you please send me an example script of doing some analysis on each frame of the trajectory and just output to a file directly.

Thanks, Bala

On Wed, Dec 23, 2009 at 6:28 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Bala, Perhaps there is a more elegant way, but you could just add the command ~dist to your per-frame script, i.e.:

distance :163@CA :166@CA ~dist

Of course, if the distance measurement is already present in Chimera, also enter the command ~dist before starting to apply the script so that the first time it runs, it will not generate that error. I hope this helps, 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 Dec 23, 2009, at 3:36 AM, Bala subramanian wrote:

Friends, I loaded a amber trajectory in chimera. I simply want to calculate the distance between two atom in each frame in the traj. and write it to a text file. I used the per-frame utility in MD movie tool.

I chose interpret script as 'chimera commands' substitute text 001-200 (frame 1 to 200)

In the script section i gave distance :163@CA :166@CA

It reports to me the following in the reply log. Distance between GLY 163 CA and ARG 166 CA: 5.083 Problem in per-frame script: Distance monitor already exists Problem in per-frame script: Distance monitor already exists Problem in per-frame script: Distance monitor already exists

How should i actually use the perframe option so that the analysis will be done in each frame and reported output file will hve the distance values for every frame. Thanks, Bala

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