[Chimera-users] Helix axis and correction

[Gulsevin, Alican]

Thanks for your quick response. I checked the source code file in the light of your response. Unfortunately, Chimera has a lot of internal variables/modules so I'm not sure whether I get the whole picture just looking at the code.

So,what I understand is that the initial calculation is used to predict the equation of the best fit line, which in turn is used as the starting point for a loop search to give the new "best" values that minimize the variance of the distance between the helix points and the best-fit line. Is my understanding correct? If so, do you take a "brute force" numerical approach to scan a number of different values and keep the best, or is that a gradient based scan? 

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
________________________________________
From: Eric Pettersen [pett at cgl.ucsf.edu]
Sent: Tuesday, November 13, 2018 3:36 PM
To: Gulsevin, Alican
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Helix axis and correction

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

Eric Pettersen
UCSF Computer Graphics Lab


On Nov 12, 2018, at 4:04 PM, Gulsevin, Alican <alican.gulsevin at Vanderbilt.Edu<mailto: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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