import sys
import modeller
import _modeller
import modeller.automodel
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): 2017/12/29 08:39:10
! wget http://www.pdb.org/pdb/files/1lmp.pdb
! wget http://www.uniprot.org/uniprot/P11941.fasta
alignm=modeller.alignment(env)
alignm.append(file='P11941.fasta', align_codes='all',alignment_format='FASTA')
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
alignm[0].code = 'model'
alignm[1].code = 'reference'
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.
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
# Выбираем объект для моделирования
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 = 1
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: 13618 12650
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 144
Number of all, selected real atoms : 1101 1101
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12650 12650
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2228
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 : 767.2455
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 : 1121 0 0 0.006 0.006 10.182 1.000
2 Bond angle potential : 1524 0 6 2.098 2.098 135.63 1.000
3 Stereochemical cosine torsion poten: 718 0 23 47.358 47.358 257.05 1.000
4 Stereochemical improper torsion pot: 460 0 1 1.393 1.393 19.108 1.000
5 Soft-sphere overlap restraints : 2228 0 0 0.002 0.002 0.66570 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) : 2404 0 0 0.098 0.098 27.134 1.000
10 Distance restraints 2 (N-O) : 2562 0 0 0.157 0.157 65.191 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: 143 0 1 4.223 4.223 30.079 1.000
14 Sidechain Chi_1 dihedral restraints: 116 0 0 51.172 51.172 2.2224 1.000
15 Sidechain Chi_2 dihedral restraints: 77 0 0 55.506 55.506 22.024 1.000
16 Sidechain Chi_3 dihedral restraints: 28 0 0 72.235 72.235 16.466 1.000
17 Sidechain Chi_4 dihedral restraints: 16 0 0 107.958 107.958 11.447 1.000
18 Disulfide distance restraints : 4 0 0 0.007 0.007 0.36894E-01 1.000
19 Disulfide angle restraints : 8 0 0 1.690 1.690 0.50442 1.000
20 Disulfide dihedral angle restraints: 4 0 0 29.987 29.987 3.4624 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) : 2049 0 0 0.397 0.397 55.082 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: 142 13 15 23.509 53.001 38.733 1.000
26 Distance restraints 4 (SDCH-SDCH) : 1274 0 0 0.656 0.656 72.222 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: model.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: 13270.4141
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 3840 1M 2R C N 7 9 -70.11 -72.10 6.12 0.43 -63.00 177.35 23.49
1 2R 2R N CA 9 10 136.11 141.90 -41.10
2 3841 2R 3A C N 18 20 -73.38 -68.20 10.07 0.65 -62.50 165.53 27.67
2 3A 3A N CA 20 21 153.94 145.30 -40.90
3 3845 6V 7L C N 44 46 -128.72 -108.50 23.44 1.03 -63.50 -173.79 29.89
3 7L 7L N CA 46 47 144.38 132.50 -41.20
4 3846 7L 8L C N 52 54 -75.80 -70.70 21.98 1.48 -63.50 156.30 22.43
4 8L 8L N CA 54 55 162.98 141.60 -41.20
5 3847 8L 9L C N 60 62 -70.83 -70.70 11.00 0.83 -63.50 166.36 23.53
5 9L 9L N CA 62 63 152.60 141.60 -41.20
6 3849 10V 11A C N 75 77 -171.71 -134.00 41.60 0.94 -62.50 -170.76 36.77
6 11A 11A N CA 77 78 164.56 147.00 -40.90
7 3851 12V 13A C N 87 89 -121.48 -134.00 19.53 1.17 -62.50 167.82 30.66
7 13A 13A N CA 89 90 161.99 147.00 -40.90
8 3852 13A 14S C N 92 94 -19.52 -72.40 60.60 3.31 -64.10 163.97 14.96
8 14S 14S N CA 94 95 122.80 152.40 -35.00
9 3853 14S 15A C N 98 100 -121.70 -134.00 12.49 0.34 -62.50 -175.93 33.32
9 15A 15A N CA 100 101 144.81 147.00 -40.90
10 3854 15A 16K C N 103 105 -96.13 -118.00 30.10 1.05 -62.90 162.66 19.55
10 16K 16K N CA 105 106 118.42 139.10 -40.80
11 3889 50E 51S C N 377 379 -140.16 -64.10 87.09 8.77 -64.10 87.09 8.77
11 51S 51S N CA 379 380 7.41 -35.00 -35.00
12 3955 116D 117P C N 884 886 -68.29 -64.50 31.72 2.57 -58.70 146.52 11.35
12 117P 117P N CA 886 887 115.70 147.20 -30.50
13 3956 117P 118N C N 891 893 148.89 -63.20 147.95 22.55 -63.20 147.95 22.55
13 118N 118N N CA 893 894 -44.14 -41.10 -41.10
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 2 15 33 70 89 110 107 134 167 196
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
model.B99990001.pdb 767.24548
import nglview
import ipywidgets
nglview.show_structure_file('model.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.
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alignm.append_sequence(''.join([i.code for i in alignm[0].residues])+'...')
alignm[2]
s = alignm[2]
pdb = alignm[1]
s.code = 'model_ligand'
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
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 = 1
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: 18 144
atom names : C +N
atom indices : 1099 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 18 144
atom names : C CA +N O
atom indices : 1099 1095 0 1100
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: 15019 14051
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 : 1144 1144
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 14051 14051
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2429
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 : 963.8503
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 : 1121 0 0 0.006 0.006 12.828 1.000
2 Bond angle potential : 1524 0 8 2.245 2.245 154.91 1.000
3 Stereochemical cosine torsion poten: 718 0 25 47.980 47.980 264.02 1.000
4 Stereochemical improper torsion pot: 460 0 0 1.504 1.504 22.132 1.000
5 Soft-sphere overlap restraints : 2429 1 2 0.008 0.008 17.331 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) : 2404 0 0 0.112 0.112 37.576 1.000
10 Distance restraints 2 (N-O) : 2562 0 6 0.200 0.200 102.01 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: 143 0 2 4.605 4.605 35.764 1.000
14 Sidechain Chi_1 dihedral restraints: 116 0 2 63.810 63.810 26.843 1.000
15 Sidechain Chi_2 dihedral restraints: 77 0 1 56.431 56.431 29.914 1.000
16 Sidechain Chi_3 dihedral restraints: 28 0 0 81.026 81.026 17.727 1.000
17 Sidechain Chi_4 dihedral restraints: 16 0 0 68.059 68.059 10.692 1.000
18 Disulfide distance restraints : 4 0 0 0.015 0.015 0.14792 1.000
19 Disulfide angle restraints : 8 0 0 1.760 1.760 0.54722 1.000
20 Disulfide dihedral angle restraints: 4 0 0 24.460 24.460 2.3209 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) : 2049 0 0 0.458 0.458 74.731 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: 142 12 19 20.783 53.272 27.998 1.000
26 Distance restraints 4 (SDCH-SDCH) : 1274 0 2 0.812 0.812 114.89 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.029 0.029 11.462 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: model_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: 14802.3887
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 3840 1M 2R C N 7 9 -68.11 -72.10 4.81 0.41 -63.00 174.39 23.90
1 2R 2R N CA 9 10 144.59 141.90 -41.10
2 3841 2R 3A C N 18 20 -108.42 -134.00 26.08 0.69 -62.50 -176.95 32.43
2 3A 3A N CA 20 21 141.91 147.00 -40.90
3 3845 6V 7L C N 44 46 -115.52 -108.50 9.17 0.41 -63.50 -173.00 23.54
3 7L 7L N CA 46 47 138.41 132.50 -41.20
4 3846 7L 8L C N 52 54 -79.47 -108.50 48.89 2.27 -63.50 135.31 17.93
4 8L 8L N CA 54 55 93.17 132.50 -41.20
5 3847 8L 9L C N 60 62 -130.50 -108.50 24.18 1.28 -63.50 176.85 21.82
5 9L 9L N CA 62 63 122.47 132.50 -41.20
6 3849 10V 11A C N 75 77 -124.39 -134.00 20.18 0.83 -62.50 -178.95 27.39
6 11A 11A N CA 77 78 129.25 147.00 -40.90
7 3851 12V 13A C N 87 89 -101.66 -68.20 51.07 5.01 -62.50 152.73 23.44
7 13A 13A N CA 89 90 106.72 145.30 -40.90
8 3852 13A 14S C N 92 94 169.47 -136.60 55.36 1.90 -64.10 -155.04 23.97
8 14S 14S N CA 94 95 163.68 151.20 -35.00
9 3853 14S 15A C N 98 100 170.47 -134.00 62.40 1.42 -62.50 -168.24 37.98
9 15A 15A N CA 100 101 175.46 147.00 -40.90
10 3854 15A 16K C N 103 105 -84.40 -70.20 15.63 0.99 -62.90 173.60 23.78
10 16K 16K N CA 105 106 146.93 140.40 -40.80
11 3923 84T 85P C N 651 653 -46.58 -58.70 59.06 3.98 -64.50 125.79 10.36
11 85P 85P N CA 653 654 -88.30 -30.50 147.20
12 3924 85P 86G C N 658 660 -65.81 -62.40 24.46 3.50 82.20 150.19 10.89
12 86G 86G N CA 660 661 -16.98 -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 9 11 53 81 112 106 130 166 163 185
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
model_ligand.B99990001.pdb 963.85028
nglview.show_structure_file('model_ligand.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.
from ipywidgets import Numbe
!jupyter nbextension enable --py --sys-prefix widgetsnbextension
!jupyter nbconvert --to html rudakov_kirill_hw6.ipynb
Enabling notebook extension jupyter-js-widgets/extension...
Traceback (most recent call last):
File "/usr/local/bin/jupyter-nbextension", line 11, in <module>
sys.exit(main())
File "/usr/local/lib/python2.7/dist-packages/jupyter_core/application.py", line 267, in launch_instance
return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/usr/local/lib/python2.7/dist-packages/notebook/nbextensions.py", line 961, in start
super(NBExtensionApp, self).start()
File "/usr/local/lib/python2.7/dist-packages/jupyter_core/application.py", line 256, in start
self.subapp.start()
File "/usr/local/lib/python2.7/dist-packages/notebook/nbextensions.py", line 869, in start
self.toggle_nbextension_python(self.extra_args[0])
File "/usr/local/lib/python2.7/dist-packages/notebook/nbextensions.py", line 845, in toggle_nbextension_python
logger=self.log)
File "/usr/local/lib/python2.7/dist-packages/notebook/nbextensions.py", line 459, in enable_nbextension_python
logger=logger)
File "/usr/local/lib/python2.7/dist-packages/notebook/nbextensions.py", line 380, in _set_nbextension_state_python
for nbext in nbexts]
File "/usr/local/lib/python2.7/dist-packages/notebook/nbextensions.py", line 345, in _set_nbextension_state
cm.update(section, {"load_extensions": {require: state}})
File "/usr/local/lib/python2.7/dist-packages/traitlets/config/manager.py", line 87, in update
self.set(section_name, data)
File "/usr/local/lib/python2.7/dist-packages/traitlets/config/manager.py", line 76, in set
f = open(filename, 'wb')
IOError: [Errno 13] Permission denied: u'/usr/etc/jupyter/nbconfig/notebook.json'
[NbConvertApp] Converting notebook rudakov_kirill_hw6.ipynb to html
[NbConvertApp] ERROR | Notebook JSON is invalid: {u'model_id': u'75ca311800f04b2281cb8731eb8598e3', u'version_minor': 0, u'version_major': 2} is not valid under any of the given schemas
Failed validating u'oneOf' in display_data[u'properties'][u'data'][u'patternProperties'][u'^(?!application/json$)[a-zA-Z0-9]+/[a-zA-Z0-9\\-\\+\\.]+$']:
On instance[u'cells'][11][u'outputs'][0][u'data'][u'application/vnd.jupyter.widget-view+json']:
{u'model_id': u'75ca311800f04b2281cb8731eb8598e3',
u'version_major': 2,
u'version_minor': 0}
[NbConvertApp] Writing 294267 bytes to rudakov_kirill_hw6.html