Hi Enrico, This is because of the coordinate averaging from the smoothing. Consider a methyl group that spins 180° between two frames if those frames get averaged — the hydrogens will all average to the same position. A similar thing can happen with ring flipping. To avoid this the smoothing would have to be for bond distances, angles and torsions instead of just coordinates. That kind of averaging is considerably more complex (and much slower to compute). My advice would be to hide hydrogens during playback. —Eric
On Nov 23, 2024, at 10:35 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users!
In visualizing the MD trajectory, I noticed a small issue with the depiction of the rapid rotations of the ligand's methyl groups. Specifically, the hydrogens appear to periodically collapse into a singularity before returning to their expected positions. Could this be addressed through additional post-processing of the trajectory data?
Many thanks in advance
Enrico _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/