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

felipe vasquez anfelvas at gmail.com
Thu May 30 12:43:41 PDT 2013


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?

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
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