Re: [PyMOL] Calculate RMSD between ligands from a crystal structure and from a docking

[Thomas H. <tho...@sc...>]

Hi Baptiste,

These files look good to me, I get:

PyMOL>rms Crystal_Rfp, Vina_Rfp
 Executive: RMSD =    0.032 (51 to 51 atoms)

Is it possible that you tried with a multi-model (multiple poses) pdbqt file before? If that's the case, specify "mobile_state" and/or "target_state":

PyMOL>rms Crystal_Rfp, Vina_Rfp, mobile_state=1, target_state=1
 Executive: RMSD =    0.032 (51 to 51 atoms)

See also "Notes" section here: https://pymolwiki.org/index.php/Align#Notes

Cheers,
  Thomas

> On Jul 26, 2018, at 9:42 AM, Baptiste Legrand <bap...@gm...> wrote:
> 
> Thanks for your answers. The molecule is the rifampicin. Please find attached the pdb from the crystal structure and the pdbqt from autodock vina. May be the format of one or both files is not correct.
> 
> Best,
> 
> Baptiste
> 
> 
> Le 25/07/2018 à 18:57, Markus Heller a écrit :
>> Not knowing what your molecule looks like, could it be automorphism?
>> 
>>> -----Original Message-----
>>> From: Baptiste Legrand <bap...@gm...>
>>> Sent: Wednesday, July 25, 2018 9:17 AM
>>> To: pym...@li...
>>> Subject: [PyMOL] Calculate RMSD between ligands from a crystal structure and
>>> from a docking
>>> 
>>> 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

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.