Hi Alex, These are not ChimeraX commands, so you must be using some other program! Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Jul 9, 2024, at 7:34 AM, Alexander Lee via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Currently, I have these commands to calculate the closest 5 :SIA out of 45 to a binding site each frame

parm ../2_md/CPLX_Neut_Sol.parm7

trajin ../2_md/10.1.produ.nc

rms :1-1469 first # align receptor

closest 5 :132-134 solventmask :SIA closestout SIA2ChainA_Binding_sites.dat name SIA

run

exit

The output file contains

Frame Molecule Distance FirstAtom#

which to my understanding, the distance is from the :SIA atom closest to the center of mass of the residues :132-134. • Is there some way to do the distance from center of mass :SIA to center of mass residues instead? • ex: [distance of closest :SIA atom to residues] > [distance of :SIA center of mass to residues] • Is there a way to do RMSD calculation of those selected closest ligands to a pdb reference? I was thinking along the lines of "for FRAME in" maybe?

Thank you, Alex