[Chimera-users] Occupancy clusters

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 16 09:31:57 PDT 2021

Hi Yasser,
The MD Movie tool has a clustering analysis, RMSD analysis, and occupancy analysis, but they are three separate calculations.  See those sections in the MD Movie help:

Only the clustering analysis gives representative frames, and it allows you to select which atoms to use.  However, since it uses best-fit RMSDs and the ligand is a rigid body, it may not be useful for your situation.

You might be able to hand-select representative frames by stepping through the movie while the occupancy isosurfaces are shown, or by trying the RMSD analysis using the option to restrict to current selection (ligand) and looking at the resulting RMSD map.

However, if those aren't feasible or useful, you may need to use some other program (I don't know which, sorry) that is tailored to analyzing moleculaar docking results, such as clustering ligand poses.
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 16, 2021, at 1:38 AM, Yasser Almeida <yasser.almeida at gmail.com> wrote:
> Hello,
> I want to do an occupancy analysis of a rigid ligand in a MD trajectory. I used the MD Movie > Analysis > Calculate occupancy tool, and obtained the volume maps of each heavy atom of the ligand. To check, I also used the gmx spatial tool from GROMACS and the VolMap from VMD, to obtain the grids for the whole ligand, which have basically the same shape.
> This grid has a characteristic shape showing that particular orientations are stable through the MD run. I want to extract representative structures of these orientations, something like an "occupancy clustering". Note that I say orientations and not conformations. Since the ligand is rigid, there is no point to calculate the RMSD. So, what I want is to calculate clusters of orientations of the ligand in the binding site.
> Is this possible with Chimera?
> Thanks in advance,
> -Yasser
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