I use the Gerardware program lsqman for this. Workflow would be something like:

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@gmail.com> wrote:

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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