Re: [PyMOL] How to calculate Hinge angle

[Sampson, J. <Jar...@ny...>]

Hi Shoeib -

It’s hard to say exactly what you need, because it will vary depending on your specific case.

If you’re looking for the change in a hinge angle between two structures of multi-domain proteins A and B, you can first superimpose domain 1 of B to domain 1 of A, get the matrix of B, superimpose domain 2 of B to domain 2 of A, get the second matrix, then use transformation.py<http://www.pymolwiki.org/index.php/Transformations> to calculate the axis and angle of that transformation.  Also see this thread http://sourceforge.net/p/pymol/mailman/message/25398209/ for more info.

If it has a standard hinge definition, perhaps something like the elbow angle<http://www.pymolwiki.org/index.php/Elbow_angle> of antibody Fab fragments, you may be able to calculate it directly from one structure, but, again, the details of that calculation will depend on your specific protein.

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Nov 2, 2014, at 10:02 PM, Shoeib Moradi <sho...@mo...<mailto:sho...@mo...>> wrote:

Dear All

I am wondering if you know how to calculate "Hinge Angle" between 2 domains of a protein?

I am not quite sure how to calculate "Center of mass" of protein and then calculating the hinge angle.

Any help is appreciated.

Regards

Shoeib


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