[Chimera-users] How to calculate the deviation of two ligands in the same pocket

Elaine Meng meng at cgl.ucsf.edu
Fri May 31 10:39:40 PDT 2013

Hi Andrés,
The "rmsd" command calculates RMSD in the current positions, without moving any atoms to fit.  See:


MatchMaker  only uses the CA atoms of the protein chains in fitting and in calculating the RMSD, so the value from MatchMaker wouldn't tell you anything about the ligand.  Instead, you might use MatchMaker first to superimpose the proteins, if they aren't already superimposed, and then use the "rmsd" command to compare the resulting two ligand positions.

Explanation of the different superposition methods in Chimera and how they work:

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

On May 30, 2013, at 12:43 PM, felipe vasquez <anfelvas at gmail.com> wrote
> Hi,
> I am working on the modeling of one ligand in a native and mutant receptor. The ligand occupies different positions in the binding cavity, and I am interested in estimate this difference. However, if RMSD is calculated via MatchMaker, the ligand in mutant receptor (non-reference) is moved from its original position to try to minimize the deviation compared to ligand in native receptor (reference). How can I calculate the difference in the ligand position between the two receptors, in an appropriate manner?
> Andrés Felipe Vásquez J., MSc.
> Grupo de Fisiología Molecular
> Instituto Nacional de Salud
> Avenida calle 26 No. 51-20 - Zona 6 CAN
> Bogotá, D.C., Colombia 

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