[Chimera-users] calculating interphosphate distance

[Eric Pettersen]

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

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