Hello all,
I am working on a project where I need to make measurements of membrane
geometry in the presence of a protein.
The problem I am having is that when I attempt to align the protein using
the rms function in cpptraj (or pytraj) with the protein as a the reference
mask, it ends up tilting the membrane. This complicates some future
measurements I am doing.
What I would like to be able to do is tell the rms function to only apply
rotations about the z-axis. I.e. only apply rotations that do not change
the z-coordinates of atoms. Does anyone know of a way to do this
efficiently within cpptraj (or pytraj)?
If need be I can always do norotate and then manually perform the z-axis
rotation in python, but I would like to avoid re-inventing the wheel, so to
speak, if possible.
Thanks in advance,
-Dr. Wesley Botello-Smith
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Received on Tue Sep 11 2018 - 13:30:02 PDT
