[Chimera-users] Helix axis and correction

Eric Pettersen pett at cgl.ucsf.edu
Tue Nov 13 13:36:46 PST 2018

Hi Alican,
	It’s an ad hoc method.  Generally speaking, without correction the helical axis vector is taken to be the largest eigenvector of the helical backbone atoms.  For short helices, this vector may differ significantly from what it would be if the helix were longer because of a “partial turn” on the end of the short helix causing the eigenvector to tilt towards those “extra” atoms.  In fact, for very short helices the largest eigenvector may not even be the best one to use — it could be going across the helix instead of along it.
	Anyway, with helical correction “on" each eigenvector is evaluated to see which has the least variance in the distances from the helical backbone atoms to the vector — the one with the least total variance is used as the initial helix axis.  Then a “corrected” axis is computed that tries to move the axis so that it has less variance, basically by having the axis “pulled” toward backbone atoms depending on the amount of variance to them.  The corrected axis then evaluated for variance, and if the variance is less, then the corrected axis is accepted as the new helical axis.  The process is repeated until no variance reduction occurs.
	The code for this is the “while iterate:” loop in the axis() function of <your Chimera installation>/share/lib/StructMeasure/__init__.py.  On a Mac, <your Chimera installation> is Chimera.app/Contents/Resources.


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Nov 12, 2018, at 4:04 PM, Gulsevin, Alican <alican.gulsevin at Vanderbilt.Edu> wrote:
> Hello everyone,
> I have a question about the "helical correction" option for calculating helix axes. I've been trying to find the exact calculation Chimera uses to correct the helix axis, but I couldn't find anything specific in the archives and I also couldn't figure it from the source code. Where can I find a detailed description of how the helix axes and the corresponding corrections are calculated?
> Thanks for your help,
> Alican Gulsevin, PhD
> Postdoctoral Researcher 
> Vanderbilt University
> Department of Chemistry
> Center for Structural Biology - Meiler Laboratory
> 465 21st Ave South
> Nashville, TN,37221
> Office: MRBIII, Room: 5150C
> Phone: (615)-936-6594
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