Re: [ccp4bb] software to get helix angles, kinks, and distances?

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: software to get helix angles, kinks, and distances?
From: "Borhani, David" David {- dot -} Borhani {- at -} DESHAWRESEARCH {- dot -} COM
Date: 2008-09-16

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Subject: Re: software to get helix angles, kinks, and distances?
From: Miles Pufall mpufall {- at -} CMP {- dot -} UCSF {- dot -} EDU
Date: 2008-09-16

Hi Natasha -

Chimera, which can be downloaded for free from: http://www.cgl.ucsf.edu/chimera/

The method for measuring the angle between two helices is here: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes

I find it intuitive and easy to use - though the exact definition of
where a helix stops and starts can have a profound effect on how the
axes of the helices are defined, and thus the angle between them.

Good luck -

Miles

On Sep 15, 2008, at 8:15 AM, Natasha Keith wrote:

> I'm sorry if this question is somewhat basic...
>
> I'm comparing three homologous proteins, and I'd like to determine a
> number of facts to be able to rigorously compare them... I'd like to
> know the angle formed by two crossed helices, the angle of kinking
> in a kinked helix, and the distance between two separated helices
> that are nearly parallel to one another along the y axis, but not
> parallel along any other axis.
>
> Could anyone recommend any software to rigorously determine
> distances and angles in differently oriented helices? My guess is
> that I'd need some kind of a program that can draw vectors through
> the helices, and find minimum distances between the vectors, or to
> use them to define angles...
>
> What do people normally use to determine these details?
>
> any suggestions would be great, thanks,
> ~Natasha Keith
> UC Berkeley
> Wemmer lab

Miles Pufall
UC San Francisco
Cellular and Molecular Pharmacology
Mail Stop 2280
600 16th Street, Genentech Hall S-574
San Francisco, California 94158-2517
(415)476-4480

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: software to get helix angles, kinks, and distances?
From: "Borhani, David" David {- dot -} Borhani {- at -} DESHAWRESEARCH {- dot -} COM
Date: 2008-09-16