hi Ahmad, To get the transformation between atomic structures that are similar but displaced from one another (without actually superimposing them), using the "match" command with "move false" and "showMatrix true" is recommended.

If a single structure includes both domains, you would open the structure twice and then in the "match" command, specify the atoms in one domain of one copy to be compared to the atoms of the other domain of the other copy. You would have to specify equal numbers of atoms in the two domains, and you could use (@ca), or backbone (@n,ca,c,o).

See explanation of "match" and its "move false" and "showMatrix true" options: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On May 27, 2021, at 1:55 PM, Kevin Jude kjude@stanford.edu wrote:

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?

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