[Chimera-users] Saving representives from ensemble cluster

James Lloyd James.Lloyd at nottingham.ac.uk
Wed Nov 18 00:21:58 PST 2020

Hi Elaine,

That is great, thanks for your help.


-------- Original message --------
From: Elaine Meng <meng at cgl.ucsf.edu>
Date: 15/11/2020 17:33 (GMT+00:00)
To: James Lloyd <pcxjl1 at exmail.nottingham.ac.uk>
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Saving representives from ensemble cluster

Hi James,
The reason for this option is to preserve spatial relationships if you have moved any models relative to each other, such as by superimposing one on the other, or moving one by hand while leaving the other frozen in place.

If you haven't moved any models relative to each other, it makes no difference whether you check this option or not.

That is why it is on by default, as it either makes no difference, or ensures that spatial relationships are preserved.

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 15, 2020, at 3:37 AM, James Lloyd <James.Lloyd at nottingham.ac.uk> wrote:
> Hi,
> I have a few Gromacs trajectories (just protein in solvent) which I have clustered using the ensemble cluster tool.
> I want to save each representive model from each cluster. However I am unsure whether these representive models need to be saved relative to another model (this option was ready ticked). Since I want to use each file separately with VinaDock, would unticking this option be wise?
> Thanks

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