Hello all,
I have a cpH-MD trajectory in which the titratable residue contains
coordinates for all possible protons. There is another file could be used
to determine which proton should be shown for each frame of trajectory, and
thus the protonation state of this residue could be determined and might
change across the entire trajectory, e.g. in the first frame the residue is
deprotonated while in the second frame the residue is protonated.
I want to use these information to show the correct protonation state for
each frame in pymol. I tried the "hide" command in pymol, but it seems to
hide atom for all states of an object.
My question is, in pymol, is possible to hide a specific atom (proton) for
a set of states while show this atom for another set of states? If yes,
what is the basic command for doing so?
Thanks in advance!
Junjun
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