In [1]:
import sys
import modeller
import _modeller
import modeller.automodel
import nglview
import ipywidgets
from IPython.display import Image
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): 2017/12/20 04:23:49
"Подопытный" - Papio anubis (Olive baboon)¶
In [3]:
! wget http://www.pdb.org/pdb/files/1lmp.pdb
! wget http://www.uniprot.org/uniprot/P61629.fasta
--2017-12-20 04:23:50-- http://www.pdb.org/pdb/files/1lmp.pdb
Resolving www.pdb.org (www.pdb.org)... 128.6.244.52
Connecting to www.pdb.org (www.pdb.org)|128.6.244.52|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://www.rcsb.org/pdb/files/1lmp.pdb [following]
--2017-12-20 04:23:50-- https://www.rcsb.org/pdb/files/1lmp.pdb
Resolving www.rcsb.org (www.rcsb.org)... 128.6.244.33
Connecting to www.rcsb.org (www.rcsb.org)|128.6.244.33|:443... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: http://files.rcsb.org/view/1lmp.pdb [following]
--2017-12-20 04:23:51-- http://files.rcsb.org/view/1lmp.pdb
Resolving files.rcsb.org (files.rcsb.org)... 132.249.213.140
Connecting to files.rcsb.org (files.rcsb.org)|132.249.213.140|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [text/plain]
Saving to: `1lmp.pdb.1'
[ <=> ] 131,301 126K/s in 1.0s
2017-12-20 04:23:53 (126 KB/s) - `1lmp.pdb.1' saved [131301]
--2017-12-20 04:23:53-- http://www.uniprot.org/uniprot/P61629.fasta
Resolving www.uniprot.org (www.uniprot.org)... 128.175.240.211, 193.62.193.81
Connecting to www.uniprot.org (www.uniprot.org)|128.175.240.211|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 217 [text/plain]
Saving to: `P61629.fasta.1'
100%[======================================>] 217 --.-K/s in 0s
2017-12-20 04:23:53 (26.6 MB/s) - `P61629.fasta.1' saved [217/217]
In [4]:
alignm=modeller.alignment(env)
In [5]:
alignm.append(file='P61629.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')
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 [6]:
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [7]:
s = alignm[0]
pdb = alignm[1]
## 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()
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: 13275 12266
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 148
Number of all, selected real atoms : 1151 1151
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12266 12266
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2334
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 : 735.2427
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 : 1174 0 0 0.006 0.006 10.652 1.000
2 Bond angle potential : 1597 0 7 2.065 2.065 136.85 1.000
3 Stereochemical cosine torsion poten: 768 0 28 47.315 47.315 268.21 1.000
4 Stereochemical improper torsion pot: 499 0 0 1.275 1.275 18.925 1.000
5 Soft-sphere overlap restraints : 2334 0 0 0.002 0.002 0.76729 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) : 2405 0 0 0.121 0.121 33.752 1.000
10 Distance restraints 2 (N-O) : 2564 0 0 0.152 0.152 65.009 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: 147 0 3 4.309 4.309 32.189 1.000
14 Sidechain Chi_1 dihedral restraints: 123 0 1 61.939 61.939 19.836 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 1 54.038 54.038 23.935 1.000
16 Sidechain Chi_3 dihedral restraints: 30 0 0 68.478 68.478 18.411 1.000
17 Sidechain Chi_4 dihedral restraints: 14 0 0 79.795 79.795 10.312 1.000
18 Disulfide distance restraints : 4 0 0 0.014 0.014 0.13412 1.000
19 Disulfide angle restraints : 8 0 0 1.820 1.820 0.58516 1.000
20 Disulfide dihedral angle restraints: 4 0 0 26.095 26.095 2.7654 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) : 1714 0 0 0.381 0.381 29.140 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: 146 12 15 19.180 50.243 17.052 1.000
26 Distance restraints 4 (SDCH-SDCH) : 982 0 0 0.581 0.581 46.721 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: sp|P61629|LYSC_PAPAN.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: 12894.4492
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 4055 1M 2K C N 7 9 -69.64 -70.20 7.50 0.56 -62.90 171.46 22.64
1 2K 2K N CA 9 10 147.87 140.40 -40.80
2 4056 2K 3A C N 16 18 -67.24 -68.20 3.15 0.29 -62.50 170.87 28.24
2 3A 3A N CA 18 19 148.30 145.30 -40.90
3 4060 6I 7L C N 44 46 -95.99 -70.70 48.76 3.02 -63.50 139.35 21.34
3 7L 7L N CA 46 47 -176.71 141.60 -41.20
4 4062 8G 9L C N 56 58 -115.32 -108.50 18.89 0.94 -63.50 176.46 27.70
4 9L 9L N CA 58 59 150.12 132.50 -41.20
5 4064 10V 11L C N 71 73 -64.50 -70.70 17.26 1.11 -63.50 166.69 23.09
5 11L 11L N CA 73 74 125.49 141.60 -41.20
6 4065 11L 12L C N 79 81 -127.76 -108.50 19.77 0.90 -63.50 -170.61 23.52
6 12L 12L N CA 81 82 136.95 132.50 -41.20
7 4066 12L 13S C N 87 89 -108.50 -136.60 31.90 0.98 -64.10 176.77 10.99
7 13S 13S N CA 89 90 136.10 151.20 -35.00
8 4070 16V 17Q C N 114 116 -99.64 -121.10 30.99 1.02 -63.80 161.67 22.05
8 17Q 17Q N CA 116 117 117.34 139.70 -40.30
9 4071 17Q 18G C N 123 125 62.04 78.70 19.44 0.63 82.20 165.80 9.05
9 18G 18G N CA 125 126 -156.07 -166.10 8.50
10 4072 18G 19K C N 127 129 -105.43 -118.00 28.59 1.17 -62.90 159.98 18.89
10 19K 19K N CA 129 130 113.42 139.10 -40.80
11 4107 53E 54S C N 415 417 -138.29 -64.10 84.74 8.56 -64.10 84.74 8.56
11 54S 54S N CA 417 418 5.94 -35.00 -35.00
12 4119 65P 66G C N 512 514 -68.72 -62.40 6.39 1.18 82.20 159.20 12.09
12 66G 66G N CA 514 515 -42.17 -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 0 6 8 45 72 103 99 122 162 173 178
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 148
Number of all, selected real atoms : 1151 1151
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12266 12266
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2372
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 : 786.1288
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 : 1174 0 0 0.006 0.006 11.728 1.000
2 Bond angle potential : 1597 0 6 2.090 2.090 140.57 1.000
3 Stereochemical cosine torsion poten: 768 0 30 47.830 47.830 276.09 1.000
4 Stereochemical improper torsion pot: 499 0 1 1.361 1.361 20.670 1.000
5 Soft-sphere overlap restraints : 2372 0 0 0.001 0.001 0.48112 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) : 2405 0 0 0.118 0.118 35.035 1.000
10 Distance restraints 2 (N-O) : 2564 0 0 0.149 0.149 64.019 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: 147 0 3 4.389 4.389 33.387 1.000
14 Sidechain Chi_1 dihedral restraints: 123 0 0 64.371 64.371 16.265 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 1 60.802 60.802 31.110 1.000
16 Sidechain Chi_3 dihedral restraints: 30 0 0 89.298 89.298 24.328 1.000
17 Sidechain Chi_4 dihedral restraints: 14 0 0 106.949 106.949 9.5508 1.000
18 Disulfide distance restraints : 4 0 0 0.006 0.006 0.22252E-01 1.000
19 Disulfide angle restraints : 8 0 0 2.745 2.745 1.3313 1.000
20 Disulfide dihedral angle restraints: 4 0 0 24.448 24.448 2.3275 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) : 1714 0 0 0.389 0.389 37.331 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: 146 12 12 20.221 52.221 20.574 1.000
26 Distance restraints 4 (SDCH-SDCH) : 982 0 0 0.640 0.640 61.314 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: sp|P61629|LYSC_PAPAN.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: 13837.7373
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 4056 2K 3A C N 16 18 -179.68 -134.00 52.21 1.21 -62.50 -172.15 36.90
1 3A 3A N CA 18 19 172.28 147.00 -40.90
2 4060 6I 7L C N 44 46 -68.83 -70.70 2.69 0.27 -63.50 175.34 24.65
2 7L 7L N CA 46 47 143.54 141.60 -41.20
3 4061 7L 8G C N 52 54 172.08 -167.20 23.81 0.77 82.20 178.62 12.67
3 8G 8G N CA 54 55 162.87 174.60 8.50
4 4064 10V 11L C N 71 73 -102.67 -108.50 28.40 1.47 -63.50 151.08 19.11
4 11L 11L N CA 73 74 104.71 132.50 -41.20
5 4065 11L 12L C N 79 81 -126.43 -108.50 34.65 1.97 -63.50 157.19 19.34
5 12L 12L N CA 81 82 102.84 132.50 -41.20
6 4066 12L 13S C N 87 89 -175.26 -136.60 45.20 1.38 -64.10 -172.99 21.57
6 13S 13S N CA 89 90 174.61 151.20 -35.00
7 4068 14V 15T C N 100 102 -152.05 -124.80 30.82 1.21 -63.20 -176.98 29.19
7 15T 15T N CA 102 103 157.90 143.50 -42.10
8 4070 16V 17Q C N 114 116 -150.44 -121.10 33.85 1.04 -63.80 -175.29 31.64
8 17Q 17Q N CA 116 117 156.57 139.70 -40.30
9 4071 17Q 18G C N 123 125 153.84 -167.20 38.96 0.75 82.20 -179.34 12.09
9 18G 18G N CA 125 126 174.35 174.60 8.50
10 4072 18G 19K C N 127 129 -126.01 -118.00 22.58 0.96 -62.90 171.05 25.99
10 19K 19K N CA 129 130 160.22 139.10 -40.80
11 4107 53E 54S C N 415 417 -138.47 -64.10 85.97 8.55 -64.10 85.97 8.55
11 54S 54S N CA 417 418 8.13 -35.00 -35.00
12 4119 65P 66G C N 512 514 -69.38 -62.40 7.12 1.21 82.20 159.10 12.04
12 66G 66G N CA 514 515 -39.81 -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 0 1 10 42 61 114 102 126 160 177 196
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
sp|P61629|LYSC_PAPAN.B99990001.pdb 735.24268
sp|P61629|LYSC_PAPAN.B99990002.pdb 786.12885
Смотрим, что получилось.¶
In [8]:
nglview.show_structure_file('sp|P61629|LYSC_PAPAN.B99990001.pdb')
Failed to display Jupyter Widget of type NGLWidget.
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In [9]:
nglview.show_structure_file('sp|P61629|LYSC_PAPAN.B99990002.pdb')
Failed to display Jupyter Widget of type NGLWidget.
If you're reading this message in Jupyter Notebook or JupyterLab, it may mean that the widgets JavaScript is still loading. If this message persists, it likely means that the widgets JavaScript library is either not installed or not enabled. See the Jupyter Widgets Documentation for setup instructions.
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In [10]:
#исходник
nglview.show_structure_file('1lmp.pdb')
Failed to display Jupyter Widget of type NGLWidget.
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Добавим лиганд.¶
In [11]:
alignm[0].residues[-3:]
Out[11]:
[Residue CYS, Residue GLY, Residue VAL]
In [12]:
pluslig = ''
for i in alignm[0].residues:
pluslig += i.code
pluslig += '...'
print (pluslig)
MKAVIILGLVLLSVTVQGKIFERCELARTLKRLGLDGYRGISLANWVCLAKWESDYNTQATNYNPGDQSTDYGIFQINSHYWCNNGKTPGAVNACHISCNALLQDNIADAVTCAKRVVSDPQGIRAWVAWRNHCQNRDVSQYVQGCGV...
In [13]:
alignm.append_sequence(pluslig)
In [14]:
alignm[2].code = 'pluslig'
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1 SALIGN_____> adding the next group to the alignment; iteration 2
In [15]:
## Выбираем объект для моделирования
s = alignm[2]
pdb = alignm[1]
In [16]:
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()
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: 18 148
atom names : C +N
atom indices : 1149 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 18 148
atom names : C CA +N O
atom indices : 1149 1145 0 1150
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: 14676 13667
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 151
Number of all, selected real atoms : 1194 1194
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13667 13667
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2623
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 : 887.1847
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 : 1174 0 0 0.006 0.006 12.375 1.000
2 Bond angle potential : 1597 0 6 2.172 2.172 149.87 1.000
3 Stereochemical cosine torsion poten: 768 0 27 47.928 47.928 273.40 1.000
4 Stereochemical improper torsion pot: 499 0 0 1.358 1.358 20.706 1.000
5 Soft-sphere overlap restraints : 2623 1 2 0.008 0.008 17.490 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) : 2405 0 0 0.121 0.121 38.746 1.000
10 Distance restraints 2 (N-O) : 2564 0 2 0.161 0.161 73.692 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: 147 0 2 4.235 4.235 31.091 1.000
14 Sidechain Chi_1 dihedral restraints: 123 0 2 75.127 75.127 39.116 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 66.949 66.949 41.915 1.000
16 Sidechain Chi_3 dihedral restraints: 30 0 0 77.716 77.716 19.184 1.000
17 Sidechain Chi_4 dihedral restraints: 14 0 0 113.341 113.341 8.5118 1.000
18 Disulfide distance restraints : 4 0 0 0.007 0.007 0.31508E-01 1.000
19 Disulfide angle restraints : 8 0 0 2.334 2.334 0.96195 1.000
20 Disulfide dihedral angle restraints: 4 0 0 29.265 29.265 2.8133 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) : 1714 0 0 0.421 0.421 47.888 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: 146 14 12 19.045 54.036 20.287 1.000
26 Distance restraints 4 (SDCH-SDCH) : 982 0 1 0.736 0.736 76.432 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.030 0.030 12.672 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: pluslig.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: 15389.7119
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 4055 1M 2K C N 7 9 -93.71 -70.20 31.70 1.90 -62.90 160.52 22.64
1 2K 2K N CA 9 10 161.66 140.40 -40.80
2 4056 2K 3A C N 16 18 -71.94 -68.20 13.92 0.99 -62.50 160.67 26.80
2 3A 3A N CA 18 19 158.71 145.30 -40.90
3 4060 6I 7L C N 44 46 -62.58 -70.70 12.68 0.79 -63.50 173.06 24.08
3 7L 7L N CA 46 47 131.86 141.60 -41.20
4 4061 7L 8G C N 52 54 92.50 78.70 35.84 0.55 82.20 152.66 7.93
4 8G 8G N CA 54 55 160.82 -166.10 8.50
5 4062 8G 9L C N 56 58 -106.47 -108.50 13.31 0.70 -63.50 166.20 21.03
5 9L 9L N CA 58 59 119.35 132.50 -41.20
6 4064 10V 11L C N 71 73 -103.25 -108.50 13.04 0.74 -63.50 178.84 27.26
6 11L 11L N CA 73 74 144.43 132.50 -41.20
7 4065 11L 12L C N 79 81 -95.80 -108.50 43.72 2.21 -63.50 135.77 17.28
7 12L 12L N CA 81 82 90.67 132.50 -41.20
8 4066 12L 13S C N 87 89 -160.70 -136.60 30.38 0.94 -64.10 -177.09 20.22
8 13S 13S N CA 89 90 169.68 151.20 -35.00
9 4068 14V 15T C N 100 102 -136.27 -124.80 13.47 0.50 -63.20 -177.41 28.21
9 15T 15T N CA 102 103 150.57 143.50 -42.10
10 4070 16V 17Q C N 114 116 -113.07 -121.10 10.77 0.55 -63.80 179.71 29.05
10 17Q 17Q N CA 116 117 146.88 139.70 -40.30
11 4071 17Q 18G C N 123 125 161.44 -167.20 31.50 0.67 82.20 -178.62 12.43
11 18G 18G N CA 125 126 171.65 174.60 8.50
12 4072 18G 19K C N 127 129 -120.31 -118.00 22.15 1.04 -62.90 168.17 25.27
12 19K 19K N CA 129 130 161.14 139.10 -40.80
13 4107 53E 54S C N 415 417 -131.21 -64.10 74.07 7.82 -64.10 74.07 7.82
13 54S 54S N CA 417 418 -3.65 -35.00 -35.00
14 4118 64N 65P C N 505 507 -69.43 -64.50 20.97 1.83 -58.70 157.68 12.18
14 65P 65P N CA 507 508 126.82 147.20 -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 0 10 16 58 91 128 123 155 155 191 184
<< 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 : 151
Number of all, selected real atoms : 1194 1194
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13667 13667
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2615
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 : 985.6867
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 : 1174 0 0 0.007 0.007 14.687 1.000
2 Bond angle potential : 1597 0 10 2.256 2.256 162.09 1.000
3 Stereochemical cosine torsion poten: 768 0 29 47.654 47.654 279.99 1.000
4 Stereochemical improper torsion pot: 499 0 0 1.401 1.401 22.143 1.000
5 Soft-sphere overlap restraints : 2615 2 2 0.008 0.008 17.834 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) : 2405 0 0 0.111 0.111 34.658 1.000
10 Distance restraints 2 (N-O) : 2564 1 6 0.207 0.207 113.73 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: 147 0 4 4.717 4.717 38.569 1.000
14 Sidechain Chi_1 dihedral restraints: 123 0 0 71.779 71.779 27.105 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 2 68.672 68.672 43.306 1.000
16 Sidechain Chi_3 dihedral restraints: 30 0 0 72.693 72.693 21.119 1.000
17 Sidechain Chi_4 dihedral restraints: 14 0 0 79.381 79.381 8.7791 1.000
18 Disulfide distance restraints : 4 0 0 0.005 0.005 0.20880E-01 1.000
19 Disulfide angle restraints : 8 0 0 2.528 2.528 1.1289 1.000
20 Disulfide dihedral angle restraints: 4 0 0 24.380 24.380 2.4044 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) : 1714 0 0 0.418 0.418 55.783 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: 146 17 17 21.196 58.505 52.273 1.000
26 Distance restraints 4 (SDCH-SDCH) : 982 0 0 0.708 0.708 77.948 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.030 0.030 12.115 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: pluslig.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: 15737.1611
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 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 8016 69S 89P N O 535 706 8.65 6.49 2.15 4.76 6.49 2.15 4.76
-------------------------------------------------------------------------------------------------
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 4055 1M 2K C N 7 9 -82.29 -70.20 18.88 1.13 -62.90 165.44 22.59
1 2K 2K N CA 9 10 154.90 140.40 -40.80
2 4056 2K 3A C N 16 18 -64.14 -68.20 4.11 0.37 -62.50 173.15 28.46
2 3A 3A N CA 18 19 145.96 145.30 -40.90
3 4060 6I 7L C N 44 46 -63.99 -70.70 16.65 1.05 -63.50 167.56 23.24
3 7L 7L N CA 46 47 126.36 141.60 -41.20
4 4061 7L 8G C N 52 54 92.38 78.70 49.56 0.89 82.20 138.14 7.22
4 8G 8G N CA 54 55 146.27 -166.10 8.50
5 4062 8G 9L C N 56 58 -111.89 -108.50 12.42 0.70 -63.50 168.84 21.21
5 9L 9L N CA 58 59 120.55 132.50 -41.20
6 4064 10V 11L C N 71 73 -122.14 -108.50 13.70 0.67 -63.50 -177.82 22.70
6 11L 11L N CA 73 74 131.29 132.50 -41.20
7 4065 11L 12L C N 79 81 -113.55 -108.50 9.27 0.53 -63.50 173.31 21.76
7 12L 12L N CA 81 82 124.73 132.50 -41.20
8 4066 12L 13S C N 87 89 -157.52 -136.60 27.54 0.86 -64.10 -178.27 19.90
8 13S 13S N CA 89 90 169.12 151.20 -35.00
9 4068 14V 15T C N 100 102 -131.74 -124.80 9.41 0.31 -63.20 -178.51 27.79
9 15T 15T N CA 102 103 149.85 143.50 -42.10
10 4070 16V 17Q C N 114 116 -152.29 -121.10 32.17 1.06 -63.80 -166.48 33.05
10 17Q 17Q N CA 116 117 147.59 139.70 -40.30
11 4071 17Q 18G C N 123 125 160.65 -167.20 33.27 0.49 82.20 -168.51 12.92
11 18G 18G N CA 125 126 -176.82 174.60 8.50
12 4072 18G 19K C N 127 129 -139.03 -118.00 23.76 0.79 -62.90 -174.61 28.63
12 19K 19K N CA 129 130 150.16 139.10 -40.80
13 4107 53E 54S C N 415 417 -138.74 -64.10 87.07 8.57 -64.10 87.07 8.57
13 54S 54S N CA 417 418 9.83 -35.00 -35.00
14 4118 64N 65P C N 505 507 -68.09 -64.50 75.86 5.47 -58.70 106.94 9.61
14 65P 65P N CA 507 508 -137.03 147.20 -30.50
15 4119 65P 66G C N 512 514 -53.48 -62.40 18.12 3.18 82.20 139.86 10.40
15 66G 66G N CA 514 515 -25.43 -41.20 8.50
16 4142 88T 89P C N 698 700 -50.44 -58.70 54.97 3.91 -64.50 128.73 10.36
16 89P 89P N CA 700 701 -84.84 -30.50 147.20
17 4143 89P 90G C N 705 707 -65.56 -62.40 26.50 3.81 82.20 149.61 10.80
17 90G 90G N CA 707 708 -14.89 -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 0 5 13 71 90 126 109 149 170 182 200
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
pluslig.B99990001.pdb 887.18469
pluslig.B99990002.pdb 985.68671
In [17]:
nglview.show_structure_file('pluslig.B99990001.pdb')
Failed to display Jupyter Widget of type NGLWidget.
If you're reading this message in Jupyter Notebook or JupyterLab, it may mean that the widgets JavaScript is still loading. If this message persists, it likely means that the widgets JavaScript library is either not installed or not enabled. See the Jupyter Widgets Documentation for setup instructions.
If you're reading this message in another notebook frontend (for example, a static rendering on GitHub or NBViewer), it may mean that your frontend doesn't currently support widgets.
In [18]:
nglview.show_structure_file('pluslig.B99990002.pdb')
Failed to display Jupyter Widget of type NGLWidget.
If you're reading this message in Jupyter Notebook or JupyterLab, it may mean that the widgets JavaScript is still loading. If this message persists, it likely means that the widgets JavaScript library is either not installed or not enabled. See the Jupyter Widgets Documentation for setup instructions.
If you're reading this message in another notebook frontend (for example, a static rendering on GitHub or NBViewer), it may mean that your frontend doesn't currently support widgets.
Не знаю, насколько корректно nglview будет отображен у Вас, так что на всякий случай приведу "доказательства" его работы у меня :)¶
In [24]:
Image(filename = "1.jpg")
Out[24]:
In [25]:
Image(filename = "2.jpg")
Out[25]:
In [26]:
Image(filename = "3.jpg")
Out[26]:
In [20]:
#импорт в html
import subprocess
converted = subprocess.call(["jupyter-nbconvert", '--to', 'html',"kovalchuk_hw6.ipynb"], shell=False)
if converted==0:
print 'Your file was sucessfully converted!'
else:
print 'Smth went wrong. for instance, check the filename...'
Your file was sucessfully converted!