[Chimera-users] interhelical angle

Eric Pettersen pett at cgl.ucsf.edu
Tue Apr 14 14:22:12 PDT 2009

Hi Sharon,
	It seems to me that there are some issues with this.  In particular  
you need the helices you are measuring to maintain their helicity  
throughout the trajectory otherwise you will get meaningless angle  
values for frames with poor helicity (the computed axis direction will  
be fairly random).  Also, to identify the helixes there have to be  
specific residues that always participate in the helix -- which I  
imagine would usually be the case but I can envision scenarios where a  
helix winds/unwinds up and down a sequence.
	Within those constraints, you can measure an inter-helical angle with  
the Python script I've attached.  You would use it in MD Movie's Per- 
Frame->Define Script dialog (choose "Python" in "Interpret script  
as").  You would need to change the specific residue numbers in the  
script to correspond to the "core" (non-unraveling) resides of your  
helices.  The angles will be printed to the Reply Log as the  
trajectory plays.
	Let me know if you have any questions/problems.

                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Apr 14, 2009, at 10:38 AM, Shuanghong Huo wrote:

> Dear Chimera Developers,
> My group needs to calculate the inter-helical angle for a large  
> trajectory.  We know Chimera can calculate the inter-helical angle  
> for a conformation.  We are wondering what the easiest way to use  
> Chimera to process the whole trajectory.  It is amber trajectory.
> Thanks,
> Sharon Huo, Ph.D.
> Associate Prof. of Chemistry & Biochemistry
> Clark University

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