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