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

[Baptiste L. <bap...@gm...>]

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
>>
>>
>>
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