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

Marko Hyvonen Thu, 26 Jul 2018 01:22:36 -0700

Hi Baptiste, removing the data at the end of the HETATM lines from ca. character 70 onwards fixed it. Not sure what these are. According to PDB 3.30 format, 67-76 should be empty. Some of the elements were non-standard also (NA for N, OA for O), but looks to be the numbers in the "empty" columns that bother PyMOL (perhaps it should just ignore these?). A lot of other things I do not recognise in PDB files in you docked rifampicin too, but those seem not to bother the analysis. See attached. RMSD 0.032 for 51 atoms. Not a bad docking pose! cheers, Marko

On 26/07/2018 08:42, Baptiste Legrand 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.legr...@gmail.com>
Sent: Wednesday, July 25, 2018 9:17 AM
To: pymol-users@lists.sourceforge.net
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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--


Marko Hyvonen
Department of Biochemistry, University of Cambridge
mh...@cam.ac.uk
+44 (0)1223 766 044
@HyvonenGroup
http://hyvonen.bioc.cam.ac.uk

MODEL 1
REMARK VINA RESULT:     -14.4      0.000      0.000
REMARK  3 active torsions:
REMARK  status: ('A' for Active; 'I' for Inactive)
REMARK    1  A    between atoms: C25_25  and  O7_46 
REMARK    2  A    between atoms: C27_27  and  O6_45 
REMARK    3  A    between atoms: C35_35  and  O7_46 
ROOT
HETATM    1  C1  RFP A   1      14.861  77.088  -1.034  1.00 64.23 
HETATM    2  C2  RFP A   1      15.023  76.669  -2.402  1.00 63.55 
HETATM    3  C3  RFP A   1      14.350  77.281  -3.488  1.00 64.11 
HETATM    4  C4  RFP A   1      13.482  78.371  -3.220  1.00 64.98 
HETATM    5  C5  RFP A   1      12.360  79.979  -1.521  1.00 63.37 
HETATM    6  C6  RFP A   1      12.216  80.372  -0.135  1.00 63.57 
HETATM    7  C7  RFP A   1      12.846  79.816   0.962  1.00 62.43 
HETATM    8  C8  RFP A   1      13.763  78.686   0.691  1.00 64.25 
HETATM    9  C9  RFP A   1      13.969  78.208  -0.751  1.00 64.46 
HETATM   10  C10 RFP A   1      13.261  78.846  -1.886  1.00 64.85 
HETATM   11  C11 RFP A   1      11.530  80.827  -2.275  1.00 64.54 
HETATM   12  C12 RFP A   1      10.836  81.777  -1.327  1.00 64.67 
HETATM   13  C13 RFP A   1      11.154  83.233  -1.636  1.00 63.87 
HETATM   14  C14 RFP A   1      12.644  80.297   2.391  1.00 61.65 
HETATM   15  C15 RFP A   1      17.186  75.435  -2.497  1.00 66.95 
HETATM   16  C16 RFP A   1      17.651  74.077  -3.017  1.00 66.71 
HETATM   17  C17 RFP A   1      16.871  72.936  -3.000  1.00 66.67 
HETATM   18  C18 RFP A   1      15.485  72.739  -2.507  1.00 65.93 
HETATM   19  C19 RFP A   1      14.676  71.814  -2.986  1.00 64.44 
HETATM   20  C20 RFP A   1      13.191  71.875  -3.353  1.00 62.92 
HETATM   21  C21 RFP A   1      12.243  72.611  -2.375  1.00 59.36 
HETATM   22  C22 RFP A   1      10.729  72.574  -2.755  1.00 59.90 
HETATM   23  C23 RFP A   1       9.769  73.317  -1.798  1.00 58.88 
HETATM   24  C24 RFP A   1       9.469  74.775  -2.193  1.00 56.87 
HETATM   25  C25 RFP A   1       8.713  75.528  -1.080  1.00 58.02 
HETATM   26  C26 RFP A   1       9.191  77.035  -0.968  1.00 57.95 
HETATM   27  C27 RFP A   1       8.186  78.065  -0.367  1.00 59.54 
HETATM   28  C28 RFP A   1       8.727  79.492  -0.297  1.00 59.95 
HETATM   29  C29 RFP A   1       8.841  80.252  -1.378  1.00 61.62 
HETATM   30  C30 RFP A   1      19.060  74.092  -3.570  1.00 64.93 
HETATM   31  C31 RFP A   1      13.117  72.440  -4.802  1.00 61.29 
HETATM   32  C32 RFP A   1      10.200  71.129  -2.936  1.00 56.29 
HETATM   33  C33 RFP A   1       8.729  74.865  -3.541  1.00 56.59 
HETATM   34  C34 RFP A   1      10.502  76.983  -0.176  1.00 57.65 
HETATM   35  C43 RFP A   1      14.504  76.857  -4.874  1.00 62.89 
HETATM   36  N1  RFP A   1      15.862  75.589  -2.711  1.00 64.57 
HETATM   37  O1  RFP A   1      15.539  76.440  -0.057  1.00 64.51 
HETATM   38  O2  RFP A   1      14.386  78.101   1.652  1.00 63.98 
HETATM   39  O3  RFP A   1      11.329  81.428   0.008  1.00 64.29 
HETATM   40  O4  RFP A   1      11.293  80.910  -3.513  1.00 68.79 
HETATM   41  O5  RFP A   1       9.388  81.582  -1.374  1.00 63.08 
HETATM   42  O9  RFP A   1      10.272  73.342  -0.426  1.00 55.51 
HETATM   43  O10 RFP A   1      12.445  72.003  -1.090  1.00 61.11 
HETATM   44  O11 RFP A   1      17.953  76.239  -1.964  1.00 69.07 
HETATM   45  O12 RFP A   1      12.868  78.905  -4.340  1.00 64.98 
ENDROOT
BRANCH  25  46
HETATM   46  O7  RFP A   1       7.226  75.420  -1.398  1.00 62.03 
BRANCH  46  47
HETATM   47  C35 RFP A   1       6.385  74.682  -0.576  1.00 60.22 
HETATM   48  C36 RFP A   1       5.051  74.563  -1.139  1.00 57.98 
HETATM   49  O8  RFP A   1       6.723  74.201   0.463  1.00 60.96 
ENDBRANCH  46  47
ENDBRANCH  25  46
BRANCH  27  50
HETATM   50  O6  RFP A   1       7.822  77.626   0.992  1.00 57.66 
HETATM   51  C37 RFP A   1       6.438  77.943   1.318  1.00 58.74 
ENDBRANCH  27  50
TORSDOF 3
ENDMDL

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

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