[chimera-dev] Finding central Axis of Strand

[Elaine Meng]

Hi Devin,
The ribbon path is based on a sliding window, so at the ends it is also using the alpha-carbon locations of the residues that are not in the strands.  So if you are just looking at the strands in your own calculation, you would not expect them to match up with the ribbon at the ends of the strands. 

Ribbon path calculation is described in the following link.  B-spline is the default.  The other method (cardinal spline) will go through all the alpha-carbon positions but then the strands will be ripply.  Both methods only use the alpha-carbons to define the path, although carbonyl O is used to define the transverse plane.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#offset>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco



> On Jul 20, 2017, at 10:10 AM, Devin Haslam <dhasl002 at odu.edu> wrote:
> 
> Hello,
> 
> I am developing my own extension to find the central axis of a strand. I am using the nitrogen atoms of a strand to estimate this line, but I have not been able to estimate the end of the strand so that it follows the ribbon. I have attached an image below that displays this error. Currently I am using the next nitrogen atom on the loop to extend my line, but I was wondering how Chimera does this with the ribbon. As you can see in the image, one end of the strand is very accurate, but the side with the arrow head has some problems. Thanks for your help.
> -- 
> Devin Haslam
> Old Dominion University, Norfolk, Virginia
> <1B5E_Twist_GreenLineGOOD.png>_______________________________________________
> Chimera-dev mailing list