Help in writing python code
Hi I am doing trajectory analysis which has 40000 frames. So for all frames I wanted to calculate the all three inertia axes. That I did. But problem is that when I run the python code it starts making all the three axes for each frames that becomes messy. So I want a little change in my code so that during trajectory analysis it should create axes but should delete or hide the previous axes also. So during run I will see only the axes which are related to that frame. Here is the python code in per-frame analysis. from chimera import runCommand frame = mdInfo['frame'] runCommand("measure inertia #1:0-120 color yellow") runCommand("measure inertia #1:120-237 color green") Thanks. Ankit
Hi Ankit, You would just use the “close” Chimera command to close the new axes model each time, e.g. “close #2” if the axes model is #2. You can see which one it is in the Model Panel (under Favorites in the menu). I would expect it to be the next unused number. Before actually running a script for a whole trajectory you should generally work out the necessary commands “by hand” (interactively) for one or two frames first. 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 Feb 5, 2015, at 8:53 PM, Ankit Agrawal <aka895@gmail.com> wrote:
Hi I am doing trajectory analysis which has 40000 frames. So for all frames I wanted to calculate the all three inertia axes. That I did. But problem is that when I run the python code it starts making all the three axes for each frames that becomes messy. So I want a little change in my code so that during trajectory analysis it should create axes but should delete or hide the previous axes also. So during run I will see only the axes which are related to that frame.
Here is the python code in per-frame analysis.
from chimera import runCommand frame = mdInfo['frame'] runCommand("measure inertia #1:0-120 color yellow") runCommand("measure inertia #1:120-237 color green")
Thanks. Ankit
Thanks. I got it. On 06-Feb-2015 9:47 pm, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Hi Ankit, You would just use the “close” Chimera command to close the new axes model each time, e.g. “close #2” if the axes model is #2. You can see which one it is in the Model Panel (under Favorites in the menu). I would expect it to be the next unused number.
Before actually running a script for a whole trajectory you should generally work out the necessary commands “by hand” (interactively) for one or two frames first.
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 Feb 5, 2015, at 8:53 PM, Ankit Agrawal <aka895@gmail.com> wrote:
Hi I am doing trajectory analysis which has 40000 frames. So for all frames I wanted to calculate the all three inertia axes. That I did. But problem is that when I run the python code it starts making all the three axes for each frames that becomes messy. So I want a little change in my code so that during trajectory analysis it should create axes but should delete or hide the previous axes also. So during run I will see only the axes which are related to that frame.
Here is the python code in per-frame analysis.
from chimera import runCommand frame = mdInfo['frame'] runCommand("measure inertia #1:0-120 color yellow") runCommand("measure inertia #1:120-237 color green")
Thanks. Ankit
participants (2)
-
Ankit Agrawal -
Elaine Meng