[Chimera-users] Transfer of the selection from reference to the ensemble

James Starlight jmsstarlight at gmail.com
Tue Jun 28 07:01:48 PDT 2016

Dear Pymol Users!

Within the Pymol session I have 2 loaded superimposed objects:
1) one experimental pdb consisted of protein with co-factors (ligand
and metals);
2) ensemble of 20 MD snapshots of the same protein (superimposed on
each others) without any cofactors;

For my particular task  I need
1) to copy the selection (which include metals and ligand atoms) from
the reference structure to each model of the MD ensemble (via Pymol),
2) make quick geometrical optimization of side-chains (I guess it
better to do it using Chimera) within the active side of each model
from MD ensemble
3) perform post-processing - analysis of the distances between
cofactors and optimized side-chains of each MD conformers to obtain
statistical distribution of averaged distances (I guess it better to
do it via some MD software like Gromacs).

I will be very thankful for any suggestions for practical realization
of those steps!


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