Re: [PyMOL] Calculate RMSD between ligands from a crystal structure and from a docking
Forget my last reply ;-) Marko is right, I didn't notice first because this is fixed in PyMOL 2.1. Some PDBQT atom types were not imported correctly in previous versions. Cheers, Thomas > On Jul 26, 2018, at 10:21 AM, Marko Hyvonen wrote: > > 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 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 > > -- > > Marko Hyvonen > Department of Biochemistry, University of Cambridge > > mh...@cam.ac.uk > > +44 (0)1223 766 044 > @HyvonenGroup > > http://hyvonen.bioc.cam.ac.uk > > -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Calculate RMSD between ligands from a crystal structure and from a docking
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 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 >>> 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 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Calculate RMSD between ligands from a crystal structure and from a docking
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
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
--
Check out the vibrant tech community on one of the world's
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sites, Slashdot.org! http://sdm.link/slashdot
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--
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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)
REMARK1 Abetween atoms: C25_25 and O7_46
REMARK2 Abetween atoms: C27_27 and O6_45
REMARK3 Abetween atoms: C35_35 and O7_46
ROOT
HETATM1 C1 RFP A 1 14.861 77.088 -1.034 1.00 64.23
HETATM2 C2 RFP A 1 15.023 76.669 -2.402 1.00 63.55
HETATM3 C3 RFP A 1 14.350 77.281 -3.488 1.00 64.11
HETATM4 C4 RFP A 1 13.482 78.371 -3.220 1.00 64.98
HETATM5 C5 RFP A 1 12.360 79.979 -1.521 1.00 63.37
HETATM6 C6 RFP A 1 12.216 80.372 -0.135 1.00 63.57
HETATM7 C7 RFP A 1 12.846 79.816 0.962 1.00 62.43
HETATM8 C8 RFP A 1 13.763 78.686 0.691 1.00 64.25
HETATM9 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
Re: [PyMOL] Calculate RMSD between ligands from a crystal structure and from a docking
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 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 -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net REMARK Accelrys Discovery Studio PDB file REMARK Created: 2018-07-19T10:09:11Z CRYST1 91.537 91.537 85.504 90.00 90.00 90.00 P43212 HETATM1 C1 RFP A 1 14.806 77.125 -1.210 1.00 64.23 C HETATM2 C2 RFP A 1 14.953 76.751 -2.593 1.00 63.55 C HETATM3 C3 RFP A 1 14.241 77.375 -3.647 1.00 64.11 C HETATM4 C4 RFP A 1 13.348 78.432 -3.331 1.00 64.98 C HETATM5 C5 RFP A 1 12.215 79.956 -1.564 1.00 63.37 C HETATM6 C6 RFP A 1 12.088 80.304 -0.164 1.00 63.57 C HETATM7 C7 RFP A 1 12.755 79.735 0.904 1.00 62.43 C HETATM8 C8 RFP A 1 13.698 78.640 0.582 1.00 64.25 C HETATM9 C9 RFP A 1 13.888 78.210 -0.877 1.00 64.46 C HETATM 10 C10 RFP A 1 13.141 78.861 -1.979 1.00 64.85 C HETATM 11 C11 RFP A 1 11.347 80.802 -2.276 1.00 64.54 C HETATM 12 C12 RFP A 1 10.646 81.703 -1.287 1.00 64.67 C HETATM 13 C13 RFP A 1 10.916 83.176 -1.558 1.00 63.87 C HETATM 14 C14 RFP A 1 12.568 80.168 2.350 1.00 61.65 C HETATM 15 C15 RFP A 1 17.147 75.583 -2.766 1.00 66.95 C HETATM 16 C16 RFP A 1 17.640 74.255 -3.335 1.00 66.71 C HETATM 17 C17 RFP A 1 16.893 73.092 -3.337 1.00 66.67 C HETATM 18 C18 RFP A 1 15.523 72.841 -2.824 1.00 65.93 C HETATM 19 C19 RFP A 1 14.731 71.908 -3.315 1.00 64.44 C HETATM 20 C20 RFP A 1 13.238 71.937 -3.652 1.00 62.92 C HETATM 21 C21 RFP A 1 12.289 72.616 -2.635 1.00 59.36 C HETATM 22 C22 RFP A 1 10.769 72.547 -2.987 1.00 59.90 C HETATM 23 C23 RFP A 1 9.808 73.234 -1.990 1.00 58.88 C HETATM 24 C24 RFP A 1 9.459 74.694 -2.336 1.00 56.87 C HETATM 25 C25 RFP A 1 8.704 75.392 -1.187 1.00 58.02 C HETATM 26 C26 RFP A 1 9.142 76.908 -1.039 1.00 57.95 C HETATM 27 C27 RFP A 1 8.120 77.890 -0.389 1.00 59.54 C HETATM 28 C28 RFP A 1 8.622 79.330 -0.286 1.00 59.95 C HETATM 29 C29 RFP A 1 8.694 80.124 -1.346 1.00 61.62 C HETATM 30 C30 RFP A 1 19.036 74.327 -3.914 1.00 64.93 C HETATM 31 C31 RFP A 1 13.119 72.542 -5.082 1.00 61.29 C HETATM 32 C32 RFP A 1 10.278 71.093 -3.201 1.00 56.29 C HETATM 33 C33 RFP A 1 8.690 74.802 -3.666 1.00 56.59 C HETATM 34 C34 RFP A 1 10.469 76.870 -0.274 1.00 57.65 C HETATM 35 C35 RFP A 1 6.399 74.521 -0.626 1.00 60.22 C HETATM 36 C36 RFP A 1 5.021 74.498 -1.088 1.00 57.98 C HETATM 37 C37 RFP A 1 6.396 77.619 1.303 1.00 58.74 C HETATM 38 C43 RFP A 1 14.380 76.997 -5.048 1.00 62.89 C HETATM 39 N1 RFP A 1 15.815 75.705 -2.950 1.00 64.57 N HETATM 40 O1 RFP A 1 15.521 76.469
Re: [PyMOL] Calculate RMSD between ligands from a crystal structure and from a docking
Not knowing what your molecule looks like, could it be automorphism? > -Original Message- > From: Baptiste Legrand > 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 > > > > -- > Check out the vibrant tech community on one of the world's most engaging tech > sites, Slashdot.org! http://sdm.link/slashdot > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
