[Chimera-users] Quantify the movement between two domains

Kevin Jude kjude at stanford.edu
Thu May 27 13:55:42 PDT 2021

I use the Gerardware program lsqman for this. Workflow would be something
REad in structure 1
REad in structure 2
calculate the operator to transform structure 2, domain 1 onto structure 1,
domain 1 (EXplicit command)
APply the matrix
Calculate the operator to transform structure 2, domain 2 onto structure 1,
domain 2 (EXplicit command)
SHow the operator - this will list several potentially useful ways to
describe the motion of domain 2, including a rotation matrix, translation
vector, rotation angle, etc.

You can probably get these measurements in other software like Chimera or
pymol, but old habits die hard. Gerard Kleywegt's programs are now hosted
at https://github.com/martynwinn/Uppsala-Software-Factory.

Kevin Jude, PhD (he/him/his)
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431

On Thu, May 27, 2021 at 1:01 PM Ahmad Khalifa <underoath006 at gmail.com>

> Hi,
> I'm looking for a way to quantify the movement between two domains in my
> structure. I know I can calculate an RMSD between the same domains in
> different conformations. I can also generate a distance matrix between the
> two chains in different conformations.
> I tried to measure the distance between the two centers of mass of
> my domains, but the change doesn't really capture the magnitude of the
> movement, also the same domains are not identical in the two conformations
> in the sense that one domain is missing so many loops, which will affect
> the com calculation.
> What other ways to quantify the distance between two different domains?
> Thank you.
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