[Chimera-users] Analysis of dihedral angles

Eric Pettersen pett at cgl.ucsf.edu
Mon Apr 12 17:26:01 PDT 2010

On Apr 12, 2010, at 9:12 AM, eduardo.troche at uvigo.es wrote:

> Hi all,
> I'm a new Chimera user. I'm performing some molecular dynamics with  
> a more or less simple system with Amber,and now that I have them  
> done, I would like to analyze some specific data,like changes in a  
> dihedral angle during the dynamic process, or distances between  
> pairs of atoms. If I select several dihedral angles in Chimera and I  
> play the dynamic movie, I can see these changes, but is it possible  
> to get a table of results that shows the value of this angle for  
> each step of the dynamic process?

Hi Eduardo,
	You can get this information by defining some actions to perform at  
each frame.  To do this use MD Movie's Per Frame->Define Script...  
menu item.  This will bring up a dialog that allows you to define  
Chimera commands or Python code to execute at each frame (controlled  
with the "Interpret script as..." menu at the top of the per-frame  
dialog).  The Chimera command "angle" can be used to report dihedrals  
to the reply log, so something like:

	angle #0:5 at o4',c1',n9,c4

would report the specified dihedral angle to the reply log.  Something  
similar can be done with the "distance" command but it's a little  
trickier since the distance command sets up a distance monitor and it  
won't let you set up a duplicate monitor, so you need to clear  
existing distance monitors first (with "~dist").  So something like  

	~dist all
	dist #0:6 at o4',h8

would report the given distance to the reply log.  If you are  
reporting many distances/angles you might consider using the "echo"  
command to insert additional text into the reply log to help you keep  
track of things.  Also, you can use the "help" command (e.g. "help  
echo") to get more info on any command.
	I hope this helps.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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