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