Tikhonova Polina. Homework 6.
In [1]:
import sys
import modeller
import _modeller
import modeller.automodel
import nglview
In [2]:
env=modeller.environ()
env.io.hetatm=True
MODELLER 9.19, 2017/07/19, r11078
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2017 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux shadbox 3.2.0-29-generic x86_64
Date and time of compilation : 2017/07/19 14:40:43
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2017/12/08 14:00:06
Взяла белок ли́сого кузу́ (или щёткохвост, или лисовидный поссум, или обыкновенный кузу-лиса — млекопитающее семейства кускусовых).
In []:
! wget http://www.pdb.org/pdb/files/1lmp.pdb
! wget http://www.uniprot.org/uniprot/P51782.fasta
In [3]:
alignm=modeller.alignment(env)
In [4]:
alignm.append(file='P51782.fasta', align_codes='all',alignment_format='FASTA')
## создадим модель
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
## и добавим в выравнивание
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
alignm[0].code = 'without_ligand'
read_pd_459W> Residue type NAG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
rdpdb___459W> Residue type NDG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
In [5]:
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
alignm[0].code = 'without_ligand'
SALIGN_____> adding the next group to the alignment; iteration 1
In [6]:
s = alignm[0]
pdb = alignm[1]
print s.code, pdb.code
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='all_in_one.ali', knowns= pdb.code , sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
without_ligand 1lmp
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
read_to_681_> topology.submodel read from topology file: 3
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 4
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 13014 11982
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 147
Number of all, selected real atoms : 1179 1179
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11982 11982
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2358
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 790.6201
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1205 0 0 0.006 0.006 12.310 1.000
2 Bond angle potential : 1624 0 5 1.969 1.969 127.56 1.000
3 Stereochemical cosine torsion poten: 773 0 36 48.801 48.801 280.90 1.000
4 Stereochemical improper torsion pot: 506 0 0 1.244 1.244 18.239 1.000
5 Soft-sphere overlap restraints : 2358 0 0 0.001 0.001 0.54846 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2380 0 3 0.146 0.146 42.705 1.000
10 Distance restraints 2 (N-O) : 2535 0 0 0.183 0.183 73.640 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 146 0 1 4.219 4.219 30.652 1.000
14 Sidechain Chi_1 dihedral restraints: 125 0 0 61.593 61.593 8.5635 1.000
15 Sidechain Chi_2 dihedral restraints: 98 0 0 75.037 75.037 37.092 1.000
16 Sidechain Chi_3 dihedral restraints: 40 0 1 84.580 84.580 28.607 1.000
17 Sidechain Chi_4 dihedral restraints: 19 0 0 81.349 81.349 11.549 1.000
18 Disulfide distance restraints : 4 0 0 0.006 0.006 0.27971E-01 1.000
19 Disulfide angle restraints : 8 0 0 1.711 1.711 0.51698 1.000
20 Disulfide dihedral angle restraints: 4 0 0 28.648 28.648 3.2186 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1577 0 0 0.395 0.395 23.522 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 145 16 20 22.136 57.429 44.195 1.000
26 Distance restraints 4 (SDCH-SDCH) : 793 0 0 0.725 0.725 46.776 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: without_ligand.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 14269.7188
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4127 3V 4L C N 23 25 -118.82 -108.50 44.55 2.29 -63.50 153.29 24.71
1 4L 4L N CA 25 26 175.84 132.50 -41.20
2 4129 5L 6L C N 39 41 -152.04 -108.50 43.82 2.15 -63.50 -169.46 23.34
2 6L 6L N CA 41 42 127.52 132.50 -41.20
3 4130 6L 7L C N 47 49 -133.26 -108.50 28.57 1.54 -63.50 174.05 21.41
3 7L 7L N CA 49 50 118.25 132.50 -41.20
4 4131 7L 8G C N 55 57 69.34 78.70 15.64 0.79 82.20 173.34 7.76
4 8G 8G N CA 57 58 -178.63 -166.10 8.50
5 4132 8G 9F C N 59 61 -132.74 -124.20 12.89 0.36 -63.20 176.98 29.11
5 9F 9F N CA 61 62 152.95 143.30 -44.30
6 4134 10I 11F C N 78 80 -99.40 -124.20 40.70 1.19 -63.20 159.49 19.86
6 11F 11F N CA 80 81 111.03 143.30 -44.30
7 4136 12C 13S C N 95 97 -78.33 -72.40 14.05 0.66 -64.10 160.49 12.53
7 13S 13S N CA 97 98 165.14 152.40 -35.00
8 4137 13S 14M C N 101 103 -72.52 -73.00 6.59 0.45 -63.40 170.17 26.12
8 14M 14M N CA 103 104 149.57 143.00 -40.50
9 4138 14M 15A C N 109 111 -125.52 -134.00 10.68 0.59 -62.50 177.20 32.41
9 15A 15A N CA 111 112 153.49 147.00 -40.90
10 4139 15A 16A C N 114 116 -135.89 -134.00 12.49 0.66 -62.50 175.81 32.74
10 16A 16A N CA 116 117 159.34 147.00 -40.90
11 4140 16A 17H C N 119 121 -107.99 -125.60 21.78 0.97 -63.20 172.02 24.43
11 17H 17H N CA 121 122 151.62 138.80 -42.30
12 4141 17H 18G C N 129 131 128.64 78.70 52.88 2.14 82.20 174.31 10.70
12 18G 18G N CA 131 132 176.51 -166.10 8.50
13 4142 18G 19K C N 133 135 -68.65 -70.20 20.62 1.46 -62.90 160.74 20.57
13 19K 19K N CA 135 136 119.84 140.40 -40.80
14 4177 53E 54S C N 436 438 -137.47 -64.10 81.11 8.55 -64.10 81.11 8.55
14 54S 54S N CA 438 439 -0.42 -35.00 -35.00
15 4188 64N 65P C N 521 523 -73.93 -64.50 9.81 1.08 -58.70 175.66 13.32
15 65P 65P N CA 523 524 144.50 147.20 -30.50
16 4241 117I 118V C N 932 934 -61.42 -62.40 51.11 6.53 -62.40 51.11 6.53
16 118V 118V N CA 934 935 8.71 -42.40 -42.40
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 3 8 45 75 116 98 129 155 171 183
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 147
Number of all, selected real atoms : 1179 1179
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11982 11982
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2410
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 890.2857
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1205 0 0 0.006 0.006 12.352 1.000
2 Bond angle potential : 1624 0 6 2.171 2.171 152.58 1.000
3 Stereochemical cosine torsion poten: 773 0 35 49.119 49.119 287.36 1.000
4 Stereochemical improper torsion pot: 506 0 1 1.584 1.584 26.643 1.000
5 Soft-sphere overlap restraints : 2410 0 0 0.002 0.002 0.88394 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2380 0 2 0.166 0.166 57.012 1.000
10 Distance restraints 2 (N-O) : 2535 0 0 0.185 0.185 75.602 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 146 0 1 4.287 4.287 31.647 1.000
14 Sidechain Chi_1 dihedral restraints: 125 0 0 68.796 68.796 24.181 1.000
15 Sidechain Chi_2 dihedral restraints: 98 0 0 70.106 70.106 36.112 1.000
16 Sidechain Chi_3 dihedral restraints: 40 0 0 79.528 79.528 31.384 1.000
17 Sidechain Chi_4 dihedral restraints: 19 0 0 90.345 90.345 12.927 1.000
18 Disulfide distance restraints : 4 0 0 0.007 0.007 0.36999E-01 1.000
19 Disulfide angle restraints : 8 0 0 1.723 1.723 0.52438 1.000
20 Disulfide dihedral angle restraints: 4 0 0 29.770 29.770 3.3614 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1577 0 0 0.438 0.438 27.315 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 145 17 18 24.303 60.966 53.991 1.000
26 Distance restraints 4 (SDCH-SDCH) : 793 0 1 0.705 0.705 56.375 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: without_ligand.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 15682.0039
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4125 1M 2K C N 7 9 -63.80 -70.20 8.60 0.72 -62.90 173.05 22.52
1 2K 2K N CA 9 10 146.15 140.40 -40.80
2 4127 3V 4L C N 23 25 -92.58 -108.50 16.60 0.85 -63.50 -179.25 23.59
2 4L 4L N CA 25 26 137.19 132.50 -41.20
3 4128 4L 5L C N 31 33 -113.70 -108.50 27.66 1.43 -63.50 166.87 26.27
3 5L 5L N CA 33 34 159.66 132.50 -41.20
4 4129 5L 6L C N 39 41 -122.42 -108.50 14.54 0.65 -63.50 -172.61 23.39
4 6L 6L N CA 41 42 136.69 132.50 -41.20
5 4130 6L 7L C N 47 49 -93.57 -70.70 27.91 1.91 -63.50 163.98 24.59
5 7L 7L N CA 49 50 157.60 141.60 -41.20
6 4131 7L 8G C N 55 57 142.51 -167.20 50.98 0.80 82.20 -175.41 11.82
6 8G 8G N CA 57 58 -177.04 174.60 8.50
7 4132 8G 9F C N 59 61 -88.75 -71.40 75.80 6.51 -63.20 114.12 14.23
7 9F 9F N CA 61 62 66.92 140.70 -44.30
8 4134 10I 11F C N 78 80 -92.52 -71.40 53.32 4.70 -63.20 139.16 17.46
8 11F 11F N CA 80 81 91.74 140.70 -44.30
9 4136 12C 13S C N 95 97 -160.88 -136.60 34.52 1.12 -64.10 177.89 19.87
9 13S 13S N CA 97 98 175.73 151.20 -35.00
10 4137 13S 14M C N 101 103 -74.40 -73.00 20.38 1.35 -63.40 156.56 24.24
10 14M 14M N CA 103 104 163.33 143.00 -40.50
11 4138 14M 15A C N 109 111 -59.72 -68.20 37.16 2.70 -62.50 150.05 24.73
11 15A 15A N CA 111 112 109.13 145.30 -40.90
12 4139 15A 16A C N 114 116 152.02 -134.00 80.70 1.84 -62.50 -158.18 40.41
12 16A 16A N CA 116 117 179.23 147.00 -40.90
13 4140 16A 17H C N 119 121 70.70 56.30 95.74 9.74 -63.20 -137.46 36.25
13 17H 17H N CA 121 122 135.45 40.80 -42.30
14 4141 17H 18G C N 129 131 176.24 -167.20 16.92 0.26 82.20 -166.11 13.63
14 18G 18G N CA 131 132 178.06 174.60 8.50
15 4142 18G 19K C N 133 135 -91.47 -70.20 28.83 2.41 -62.90 164.24 19.94
15 19K 19K N CA 135 136 120.94 140.40 -40.80
16 4177 53E 54S C N 436 438 -137.42 -64.10 80.90 8.55 -64.10 80.90 8.55
16 54S 54S N CA 438 439 -0.81 -35.00 -35.00
17 4189 65P 66G C N 528 530 -68.85 -62.40 7.73 1.46 82.20 160.40 12.23
17 66G 66G N CA 530 531 -45.46 -41.20 8.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 4 13 49 70 112 115 128 154 201 199
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
without_ligand.B99990001.pdb 790.62006
without_ligand.B99990002.pdb 890.28571
In [7]:
nglview.show_structure_file('without_ligand.B99990001.pdb')
In [8]:
# original structure
nglview.show_structure_file('1lmp.pdb')
Find ligand code¶
In [9]:
n=20
for i in range(0,len(alignm[1].residues),n):
if (i+n) < len(alignm[1].residues):
print str('{:^5}'*n).format(*[k.name for k in alignm[1].residues[i:i+n]])
print str('{:^5}'*n).format(*[k.code for k in alignm[1].residues[i:i+n]])
else:
n = len(alignm[1].residues)-i
print str('{:^5}'*n).format(*[k.name for k in alignm[1].residues[i:len(alignm[1].residues)]])
print str('{:^5}'*n).format(*[k.code for k in alignm[1].residues[i:len(alignm[1].residues)]])
LYS VAL TYR ASP ARG CYS GLU LEU ALA ARG ALA LEU LYS ALA SER GLY MET ASP GLY TYR K V Y D R C E L A R A L K A S G M D G Y ALA GLY ASN SER LEU PRO ASN TRP VAL CYS LEU SER LYS TRP GLU SER SER TYR ASN THR A G N S L P N W V C L S K W E S S Y N T GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP TYR GLY ILE PHE GLN ILE ASN SER Q A T N R N T D G S T D Y G I F Q I N S ARG TYR TRP CYS ASP ASP GLY ARG THR PRO GLY ALA LYS ASN VAL CYS GLY ILE ARG CYS R Y W C D D G R T P G A K N V C G I R C SER GLN LEU LEU THR ASP ASP LEU THR VAL ALA ILE ARG CYS ALA LYS ARG VAL VAL LEU S Q L L T D D L T V A I R C A K R V V L ASP PRO ASN GLY ILE GLY ALA TRP VAL ALA TRP ARG LEU HIS CYS GLN ASN GLN ASP LEU D P N G I G A W V A W R L H C Q N Q D L ARG SER TYR VAL ALA GLY CYS GLY VAL NAG NAG NDG R S Y V A G C G V . . .
In [10]:
alignm2=modeller.alignment(env)
residues = ''.join([k.code for k in alignm[0].residues]) + ''.join([k.code for k in alignm[1].residues[-3:]])
alignm2.append_sequence(residues)
## создадим модель
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
## и добавим в выравнивание
alignm2.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
alignm2[0].code = 'with_ligand'
In [11]:
alignm2.salign()
alignm2.write(file='all_in_one_ligand.ali', alignment_format='PIR')
s = alignm2[0]
pdb = alignm2[1]
print s.code, pdb.code
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='all_in_one_ligand.ali', knowns= pdb.code , sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
SALIGN_____> adding the next group to the alignment; iteration 1
with_ligand 1lmp
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 10 147
atom names : C +N
atom indices : 1177 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 10 147
atom names : C CA +N O
atom indices : 1177 1172 0 1178
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 4
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 14413 13381
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 150
Number of all, selected real atoms : 1222 1222
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13381 13381
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2608
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 986.9169
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1205 0 0 0.007 0.007 17.018 1.000
2 Bond angle potential : 1624 0 6 2.201 2.201 157.57 1.000
3 Stereochemical cosine torsion poten: 773 0 36 49.331 49.331 288.41 1.000
4 Stereochemical improper torsion pot: 506 0 1 1.544 1.544 25.815 1.000
5 Soft-sphere overlap restraints : 2608 2 2 0.008 0.008 17.726 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2380 0 0 0.134 0.134 42.382 1.000
10 Distance restraints 2 (N-O) : 2535 0 0 0.180 0.180 77.130 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 146 0 1 4.076 4.076 28.608 1.000
14 Sidechain Chi_1 dihedral restraints: 125 0 4 77.022 77.022 40.143 1.000
15 Sidechain Chi_2 dihedral restraints: 98 0 2 83.185 83.185 50.228 1.000
16 Sidechain Chi_3 dihedral restraints: 40 0 0 82.143 82.143 29.844 1.000
17 Sidechain Chi_4 dihedral restraints: 19 0 0 88.836 88.836 12.418 1.000
18 Disulfide distance restraints : 4 0 0 0.015 0.015 0.15137 1.000
19 Disulfide angle restraints : 8 0 0 2.254 2.254 0.89779 1.000
20 Disulfide dihedral angle restraints: 4 0 0 23.797 23.797 2.2068 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1577 0 0 0.426 0.426 44.445 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 145 18 18 22.873 62.767 54.413 1.000
26 Distance restraints 4 (SDCH-SDCH) : 793 0 1 0.777 0.777 76.270 1.000
27 Distance restraints 5 (X-Y) : 1399 0 0 0.042 0.042 21.236 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: with_ligand.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 17066.4570
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4125 1M 2K C N 7 9 -82.94 -70.20 16.36 0.99 -62.90 169.72 23.19
1 2K 2K N CA 9 10 150.67 140.40 -40.80
2 4127 3V 4L C N 23 25 -71.22 -70.70 4.60 0.33 -63.50 172.80 24.44
2 4L 4L N CA 25 26 146.17 141.60 -41.20
3 4128 4L 5L C N 31 33 -66.46 -70.70 4.67 0.47 -63.50 175.26 24.50
3 5L 5L N CA 33 34 143.56 141.60 -41.20
4 4129 5L 6L C N 39 41 -68.34 -70.70 3.34 0.21 -63.50 179.63 25.22
4 6L 6L N CA 41 42 139.23 141.60 -41.20
5 4130 6L 7L C N 47 49 -74.07 -70.70 3.42 0.29 -63.50 176.95 25.19
5 7L 7L N CA 49 50 142.17 141.60 -41.20
6 4131 7L 8G C N 55 57 130.25 78.70 52.50 2.38 82.20 -178.09 11.15
6 8G 8G N CA 57 58 -176.04 -166.10 8.50
7 4132 8G 9F C N 59 61 -75.74 -71.40 4.34 0.29 -63.20 175.50 25.21
7 9F 9F N CA 61 62 140.65 140.70 -44.30
8 4134 10I 11F C N 78 80 -129.14 -124.20 5.80 0.15 -63.20 -178.26 29.57
8 11F 11F N CA 80 81 146.35 143.30 -44.30
9 4136 12C 13S C N 95 97 -68.42 -72.40 25.93 1.39 -64.10 161.84 11.48
9 13S 13S N CA 97 98 126.78 152.40 -35.00
10 4137 13S 14M C N 101 103 -171.86 -125.60 49.01 1.57 -63.40 -164.36 37.47
10 14M 14M N CA 103 104 156.68 140.50 -40.50
11 4138 14M 15A C N 109 111 -89.38 -68.20 42.27 4.05 -62.50 152.02 23.74
11 15A 15A N CA 111 112 108.72 145.30 -40.90
12 4139 15A 16A C N 114 116 169.77 -134.00 63.01 1.44 -62.50 -167.76 38.09
12 16A 16A N CA 116 117 175.43 147.00 -40.90
13 4140 16A 17H C N 119 121 -136.55 -125.60 67.93 2.36 -63.20 133.77 21.41
13 17H 17H N CA 121 122 -154.16 138.80 -42.30
14 4141 17H 18G C N 129 131 -76.19 -80.20 4.78 0.35 82.20 -128.97 7.00
14 18G 18G N CA 131 132 176.69 174.10 8.50
15 4142 18G 19K C N 133 135 -71.64 -70.20 14.31 1.07 -62.90 167.19 21.25
15 19K 19K N CA 135 136 126.16 140.40 -40.80
16 4177 53E 54S C N 436 438 -136.45 -64.10 80.20 8.42 -64.10 80.20 8.42
16 54S 54S N CA 438 439 -0.39 -35.00 -35.00
17 4188 64N 65P C N 521 523 -76.69 -64.50 13.49 1.09 -58.70 177.44 16.14
17 65P 65P N CA 523 524 152.98 147.20 -30.50
18 4241 117I 118V C N 932 934 -56.39 -62.40 50.23 6.72 -62.40 50.23 6.72
18 118V 118V N CA 934 935 7.47 -42.40 -42.40
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 12 14 55 76 137 129 155 177 183 210
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 150
Number of all, selected real atoms : 1222 1222
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13381 13381
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2608
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 963.2237
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1205 0 0 0.007 0.007 17.632 1.000
2 Bond angle potential : 1624 0 8 2.242 2.242 164.34 1.000
3 Stereochemical cosine torsion poten: 773 0 33 49.416 49.416 289.20 1.000
4 Stereochemical improper torsion pot: 506 0 0 1.479 1.479 23.834 1.000
5 Soft-sphere overlap restraints : 2608 2 2 0.008 0.008 18.277 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2380 0 0 0.131 0.131 40.823 1.000
10 Distance restraints 2 (N-O) : 2535 0 0 0.178 0.178 74.743 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 146 0 2 4.473 4.473 34.453 1.000
14 Sidechain Chi_1 dihedral restraints: 125 0 2 67.065 67.065 25.521 1.000
15 Sidechain Chi_2 dihedral restraints: 98 0 4 70.929 70.929 44.676 1.000
16 Sidechain Chi_3 dihedral restraints: 40 0 0 69.402 69.402 23.443 1.000
17 Sidechain Chi_4 dihedral restraints: 19 0 0 86.281 86.281 13.620 1.000
18 Disulfide distance restraints : 4 0 0 0.006 0.006 0.25204E-01 1.000
19 Disulfide angle restraints : 8 0 0 2.636 2.636 1.2271 1.000
20 Disulfide dihedral angle restraints: 4 0 0 26.145 26.145 2.6144 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1577 0 0 0.379 0.379 38.241 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 145 17 20 22.629 60.754 58.389 1.000
26 Distance restraints 4 (SDCH-SDCH) : 793 0 0 0.720 0.720 70.342 1.000
27 Distance restraints 5 (X-Y) : 1399 0 0 0.042 0.042 21.824 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: with_ligand.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 15741.5723
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4125 1M 2K C N 7 9 -81.14 -70.20 17.55 1.05 -62.90 166.10 22.61
1 2K 2K N CA 9 10 154.11 140.40 -40.80
2 4127 3V 4L C N 23 25 -114.08 -108.50 17.45 0.87 -63.50 177.14 27.71
2 4L 4L N CA 25 26 149.03 132.50 -41.20
3 4128 4L 5L C N 31 33 -70.68 -70.70 11.10 0.84 -63.50 166.25 23.50
3 5L 5L N CA 33 34 152.70 141.60 -41.20
4 4129 5L 6L C N 39 41 -64.48 -70.70 6.54 0.52 -63.50 179.23 24.94
4 6L 6L N CA 41 42 139.57 141.60 -41.20
5 4130 6L 7L C N 47 49 -99.59 -108.50 8.99 0.44 -63.50 178.57 22.98
5 7L 7L N CA 49 50 133.68 132.50 -41.20
6 4131 7L 8G C N 55 57 -167.53 -167.20 47.77 1.88 82.20 161.74 12.32
6 8G 8G N CA 57 58 126.83 174.60 8.50
7 4132 8G 9F C N 59 61 -175.75 -124.20 60.56 1.59 -63.20 -179.89 31.72
7 9F 9F N CA 61 62 175.08 143.30 -44.30
8 4134 10I 11F C N 78 80 -83.49 -71.40 40.43 3.52 -63.20 147.82 19.20
8 11F 11F N CA 80 81 102.12 140.70 -44.30
9 4136 12C 13S C N 95 97 -74.99 -72.40 16.62 0.89 -64.10 156.56 12.02
9 13S 13S N CA 97 98 168.82 152.40 -35.00
10 4137 13S 14M C N 101 103 -82.45 -73.00 71.37 4.99 -63.40 114.36 15.69
10 14M 14M N CA 103 104 72.26 143.00 -40.50
11 4138 14M 15A C N 109 111 -163.05 -134.00 29.64 0.78 -62.50 -165.70 37.20
11 15A 15A N CA 111 112 152.85 147.00 -40.90
12 4139 15A 16A C N 114 116 -64.85 -68.20 7.53 0.50 -62.50 179.47 29.30
12 16A 16A N CA 116 117 138.56 145.30 -40.90
13 4140 16A 17H C N 119 121 -136.06 -125.60 11.58 0.49 -63.20 -169.40 20.48
13 17H 17H N CA 121 122 133.82 138.80 -42.30
14 4141 17H 18G C N 129 131 -176.17 -167.20 19.38 0.79 82.20 -179.71 13.15
14 18G 18G N CA 131 132 157.42 174.60 8.50
15 4142 18G 19K C N 133 135 -81.94 -70.20 17.34 1.45 -62.90 169.51 21.04
15 19K 19K N CA 135 136 127.63 140.40 -40.80
16 4177 53E 54S C N 436 438 -134.90 -64.10 74.64 8.43 -64.10 74.64 8.43
16 54S 54S N CA 438 439 -11.35 -35.00 -35.00
17 4188 64N 65P C N 521 523 -76.19 -64.50 14.43 1.02 -58.70 174.73 15.88
17 65P 65P N CA 523 524 155.65 147.20 -30.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 8 13 58 85 144 124 137 193 197 192
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
with_ligand.B99990001.pdb 986.91687
with_ligand.B99990002.pdb 963.22369
Ngl view в html выдает почему-то некрасивую картинку
In [12]:
nglview.show_structure_file('with_ligand.B99990001.pdb')
А так она выглядит в jupyter ноутбуке.
In [65]:
nglview.show_structure_file('with_ligand.B99990001.pdb')