Dear all,
I tried to calculate a rmsd value between ligands from a crystal
structure and after docking. The two molecules share similar
nomenclatures and are really well superimposed. I think that the RMSD
should be < 1 A. I used the following lines:
alter all,segi=""
alter all,chain =""
rms /ligand_crystal////*, /ligand_docking////*
It works but I obtained an abnormal high RMSD value of 6.146 A. When I
use the pair_fit function, pymol completely return one molecule and also
write "ExecutiveRMS: RMS = 6.146 (51 to 51 atoms)". I should have
missed something...
thanks for the help,
All the Best.
Baptiste
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