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