[Chimera-users] Analysis of dihedral angles

Elaine Meng meng at cgl.ucsf.edu
Tue Apr 13 08:58:55 PDT 2010

Hi Marco,

(a) distances.  If you have Chimera 1.5 (daily build) you can use the  
findclash command to find all distances between two sets of atoms.   
The two sets can contain the same or different atoms.  For example,  
you could find all distances among NH protons or between NH protons  
and other protons.  See these previous replies:
(except note that the mail program has expanded "@" to " at "!)

(b) peptide dihedrals.  The phi,psi,chiN values for amino acid  
residues are automatically assigned as attributes.  You can save an  
attribute (list of values) to a file from the Render by Attribute tool.

Currently there is no Chimera command to save attributes, however.

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 13, 2010, at 2:24 AM, sette at uniroma2.it wrote:

> Hi all,
> my reply is not really related but similar.
> I work with NMR data and often we need list of distances or dihedral  
> angles for the whole molecule, like distances between a NH protons  
> and the rest of the molecule, or list of the chi1 dihedral angles.  
> It seems that at present there is no way to get this. Scripts are  
> possible?
> Thanks,
> Marco

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