On Feb 27, 2008, at 11:08 PM, bala wrote:
Dear chimera users,
i) Greetings. I have a trajectory of 1000 conformations of a RNA molecule. I want to see the distribution of interphosphate distance. say i want to see the P-P distance of the residue 3 paired with a residue 38 in the opposite strand. Is it possible in anyways.
ii) Suppose when i source a file from command line option : source dist, chimera nicely takes the distance commands in the file and displays the distances in the GUI. Is it possible to send the output to a file rather than seeing in GUI.
The script that 吴超 was nice enough to forward will print out distances. If not run in nogui mode (i.e. normally, with the graphical interface) the distances will go to the Reply Log, and you can save them to a file from there. Furthermore, you can use the Per- Frame->Define Script menu item of MD Movie to have the script executed each frame. You may or may not want to prefix the output with the frame number; if you do you need to put mdInfo['frame'] somewhere in the print statement. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu