Re: [AMBER] cpptraj PCA PC-mode pseudo traj

From: Daniel Roe <>
Date: Mon, 4 May 2020 16:46:52 -0400


On Mon, May 4, 2020 at 4:19 PM Schröder, David Christopher
<> wrote:
> I would like to know whether the exported frames between the maxima are real existing frames taken from the previously
> loaded trajectories and therefore can be labelled as representative structures.

No, they are frames generated by projecting the average coordinates
along the specified eigenvector (see the manual entry for the 'modes'
command). You could potentially capture representative frames by
calculating projections along the desired eigenvector (or
eigenvectors) with the 'projection' action, then filtering frames that
match desired projection values (with e.g. the 'filter' action). Hope
this helps,


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Received on Mon May 04 2020 - 14:00:02 PDT
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