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

felipe vasquez anfelvas at gmail.com
Fri May 31 12:21:10 PDT 2013

Hi Elaine,

I want to compare two different docking poses with the same ligand and
receptor. The only difference is that, in one of the receptors, it was
included a water molecule. So, as a result, the ligand occupies a vey
different position in the active site (approximately moved 2 angstroms and
rotated 180 degrees) compared to the ligand in the first receptor (without
the water molecule). Now, I want to discuss this difference in a
quantitative manner, but if I try to calculate the RMSD of the entire
docking poses, Chimera and other programs only take into account the
receptor and not the ligand, and as a result my RMSD is 0.000. Now, if I
'cut' the ligand and save it as a different file in both cases, once I try
to calculate RMSD, the original position of the ligands is lost, and I
obtain a undesirable value. Is it the estimation of RMSD appropriate
(informative) for evaluating the conformational change of my ligand to
discuss the difference in protein-ligand interaction?

Best regards,

*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

2013/5/31 Elaine Meng <meng at cgl.ucsf.edu>

> Hi Andrés,
> The "rmsd" command calculates RMSD in the current positions, without
> moving any atoms to fit.  See:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html>
> 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:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
> I hope this helps,
> Elaine
> ----------
> 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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