[Chimera-users] Request for axes measurements

Elaine Meng meng at cgl.ucsf.edu
Sun Jun 14 10:30:28 PDT 2015


Sorry, Chimera does not figure this out for you.  In other words, it does not treat axes as vectors.

After you get the positive value, you would have to look at the N->C directionality of the helices yourself to decide whether it should be converted to negative, or even kept positive but subtracted from 180.

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 Jun 14, 2015, at 7:13 AM, Jayaraman T <jram at pusan.ac.kr> wrote:

> Hi all, 
> 
> We defined axes for helices (user defined set of atoms) using axes module in Chimera and we found the angles between them are positives. 
> 
> If we do consider the axes are infinite lines and not as vector, then how could we normalize them for finding the eigenvectors/values for the selected set of atomic coordinates.
> 
> We have been trying for a while but couldn't get them clearly, please help us and it'd be grateful. 
> 
> Thank you. 
> 




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