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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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
HETATM 1 C1 RFP A 1 14.806 77.125 -1.210 1.00 64.23 C
HETATM 2 C2 RFP A 1 14.953 76.751 -2.593 1.00 63.55 C
HETATM 3 C3 RFP A 1 14.241 77.375 -3.647 1.00 64.11 C
HETATM 4 C4 RFP A 1 13.348 78.432 -3.331 1.00 64.98 C
HETATM 5 C5 RFP A 1 12.215 79.956 -1.564 1.00 63.37 C
HETATM 6 C6 RFP A 1 12.088 80.304 -0.164 1.00 63.57 C
HETATM 7 C7 RFP A 1 12.755 79.735 0.904 1.00 62.43 C
HETATM 8 C8 RFP A 1 13.698 78.640 0.582 1.00 64.25 C
HETATM 9 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 -0.266 1.00 64.51 O
HETATM 41 O2 RFP A 1 14.356 78.045 1.513 1.00 63.98 O
HETATM 42 O3 RFP A 1 11.174 81.330 0.027 1.00 64.29 O
HETATM 43 O4 RFP A 1 11.084 80.914 -3.506 1.00 68.79 O
HETATM 44 O5 RFP A 1 9.203 81.468 -1.313 1.00 63.08 O
HETATM 45 O6 RFP A 1 7.796 77.401 0.963 1.00 57.66 O
HETATM 46 O7 RFP A 1 7.215 75.250 -1.480 1.00 62.03 O
HETATM 47 O8 RFP A 1 6.787 73.976 0.362 1.00 60.96 O
HETATM 48 O9 RFP A 1 10.337 73.233 -0.628 1.00 55.51 O
HETATM 49 O10 RFP A 1 12.533 71.977 -1.373 1.00 61.11 O
HETATM 50 O11 RFP A 1 17.901 76.393 -2.224 1.00 69.07 O
HETATM 51 O12 RFP A 1 12.698 78.980 -4.422 1.00 64.98 O
TER 52 RFP A 1
CONECT 1 2 9 40
CONECT 2 1 3 39
CONECT 3 2 4 38
CONECT 4 3 10 51
CONECT 5 6 10 11
CONECT 6 5 7 42
CONECT 7 6 8 14
CONECT 8 7 9 41
CONECT 9 1 8 10
CONECT 10 4 5 9
CONECT 11 5 12 43
CONECT 12 11 13 42 44
CONECT 13 12
CONECT 14 7
CONECT 15 16 39 50
CONECT 16 15 17 30
CONECT 17 16 18
CONECT 18 17 19
CONECT 19 18 20
CONECT 20 19 21 31
CONECT 21 20 22 49
CONECT 22 21 23 32
CONECT 23 22 24 48
CONECT 24 23 25 33
CONECT 25 24 26 46
CONECT 26 25 27 34
CONECT 27 26 28 45
CONECT 28 27 29
CONECT 29 28 44
CONECT 30 16
CONECT 31 20
CONECT 32 22
CONECT 33 24
CONECT 34 26
CONECT 35 36 46 47
CONECT 36 35
CONECT 37 45
CONECT 38 3
CONECT 39 2 15
CONECT 40 1
CONECT 41 8
CONECT 42 6 12
CONECT 43 11
CONECT 44 12 29
CONECT 45 27 37
CONECT 46 25 35
CONECT 47 35
CONECT 48 23
CONECT 49 21
CONECT 50 15
CONECT 51 4
END
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 0.151 A
HETATM 2 C2 RFP A 1 15.023 76.669 -2.402 1.00 63.55 0.108 A
HETATM 3 C3 RFP A 1 14.350 77.281 -3.488 1.00 64.11 0.023 A
HETATM 4 C4 RFP A 1 13.482 78.371 -3.220 1.00 64.98 0.129 A
HETATM 5 C5 RFP A 1 12.360 79.979 -1.521 1.00 63.37 0.064 A
HETATM 6 C6 RFP A 1 12.216 80.372 -0.135 1.00 63.57 0.099 A
HETATM 7 C7 RFP A 1 12.846 79.816 0.962 1.00 62.43 0.040 A
HETATM 8 C8 RFP A 1 13.763 78.686 0.691 1.00 64.25 0.196 A
HETATM 9 C9 RFP A 1 13.969 78.208 -0.751 1.00 64.46 0.068 A
HETATM 10 C10 RFP A 1 13.261 78.846 -1.886 1.00 64.85 0.035 A
HETATM 11 C11 RFP A 1 11.530 80.827 -2.275 1.00 64.54 0.226 A
HETATM 12 C12 RFP A 1 10.836 81.777 -1.327 1.00 64.67 0.253 A
HETATM 13 C13 RFP A 1 11.154 83.233 -1.636 1.00 63.87 0.071 C
HETATM 14 C14 RFP A 1 12.644 80.297 2.391 1.00 61.65 0.036 C
HETATM 15 C15 RFP A 1 17.186 75.435 -2.497 1.00 66.95 0.275 C
HETATM 16 C16 RFP A 1 17.651 74.077 -3.017 1.00 66.71 0.036 C
HETATM 17 C17 RFP A 1 16.871 72.936 -3.000 1.00 66.67 0.000 C
HETATM 18 C18 RFP A 1 15.485 72.739 -2.507 1.00 65.93 -0.005 C
HETATM 19 C19 RFP A 1 14.676 71.814 -2.986 1.00 64.44 -0.024 C
HETATM 20 C20 RFP A 1 13.191 71.875 -3.353 1.00 62.92 0.053 C
HETATM 21 C21 RFP A 1 12.243 72.611 -2.375 1.00 59.36 0.159 C
HETATM 22 C22 RFP A 1 10.729 72.574 -2.755 1.00 59.90 0.061 C
HETATM 23 C23 RFP A 1 9.769 73.317 -1.798 1.00 58.88 0.157 C
HETATM 24 C24 RFP A 1 9.469 74.775 -2.193 1.00 56.87 0.059 C
HETATM 25 C25 RFP A 1 8.713 75.528 -1.080 1.00 58.02 0.129 C
HETATM 26 C26 RFP A 1 9.191 77.035 -0.968 1.00 57.95 0.059 C
HETATM 27 C27 RFP A 1 8.186 78.065 -0.367 1.00 59.54 0.142 C
HETATM 28 C28 RFP A 1 8.727 79.492 -0.297 1.00 59.95 0.029 C
HETATM 29 C29 RFP A 1 8.841 80.252 -1.378 1.00 61.62 0.117 C
HETATM 30 C30 RFP A 1 19.060 74.092 -3.570 1.00 64.93 0.036 C
HETATM 31 C31 RFP A 1 13.117 72.440 -4.802 1.00 61.29 0.007 C
HETATM 32 C32 RFP A 1 10.200 71.129 -2.936 1.00 56.29 0.005 C
HETATM 33 C33 RFP A 1 8.729 74.865 -3.541 1.00 56.59 0.005 C
HETATM 34 C34 RFP A 1 10.502 76.983 -0.176 1.00 57.65 0.005 C
HETATM 35 C43 RFP A 1 14.504 76.857 -4.874 1.00 62.89 0.035 C
HETATM 36 N1 RFP A 1 15.862 75.589 -2.711 1.00 64.57 -0.206 NA
HETATM 37 O1 RFP A 1 15.539 76.440 -0.057 1.00 64.51 -0.189 OA
HETATM 38 O2 RFP A 1 14.386 78.101 1.652 1.00 63.98 -0.287 OA
HETATM 39 O3 RFP A 1 11.329 81.428 0.008 1.00 64.29 -0.303 OA
HETATM 40 O4 RFP A 1 11.293 80.910 -3.513 1.00 68.79 -0.286 OA
HETATM 41 O5 RFP A 1 9.388 81.582 -1.374 1.00 63.08 -0.302 OA
HETATM 42 O9 RFP A 1 10.272 73.342 -0.426 1.00 55.51 -0.223 OA
HETATM 43 O10 RFP A 1 12.445 72.003 -1.090 1.00 61.11 -0.223 OA
HETATM 44 O11 RFP A 1 17.953 76.239 -1.964 1.00 69.07 -0.266 OA
HETATM 45 O12 RFP A 1 12.868 78.905 -4.340 1.00 64.98 -0.190 OA
ENDROOT
BRANCH 25 46
HETATM 46 O7 RFP A 1 7.226 75.420 -1.398 1.00 62.03 -0.304 OA
BRANCH 46 47
HETATM 47 C35 RFP A 1 6.385 74.682 -0.576 1.00 60.22 0.272 C
HETATM 48 C36 RFP A 1 5.051 74.563 -1.139 1.00 57.98 0.106 C
HETATM 49 O8 RFP A 1 6.723 74.201 0.463 1.00 60.96 -0.264 OA
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 -0.349 OA
HETATM 51 C37 RFP A 1 6.438 77.943 1.318 1.00 58.74 0.175 C
ENDBRANCH 27 50
TORSDOF 3
ENDMDL
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