Re: [AMBER] RMS rotate about z-axis only

From: Daniel Roe <>
Date: Thu, 20 Sep 2018 11:25:03 -0400

Hi Wesley,

Cpptraj can't do this yet, but it wouldn't be hard to implement. The
'rotate' command will take rotation matrices as input (you can get
these directly from the 'rms' command these days), so all that would
be needed is to zero the appropriate off-diagonal elements and set the
3,3 element to 1 (I think), and that would get you the rotation around
Z. I'll open up an issue on GitHub to remind me to attempt this when I
have time.

On Tue, Sep 11, 2018 at 4:03 PM Wesley Michael Botello-Smith
<> wrote:
> 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 Thu Sep 20 2018 - 08:30:05 PDT
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