Цель занятия - ознакомиться с возможностями гомологичного моделирования комплекса белка с лигандом. В этом занятии будет использоваться пакет Modeller. Используя известную структуру лизоцима форели как образец, построим модель комплекса белка лизоцима тутового шелкопряда LYS_BOMMO с лигандом. Скачаем заготовку из PDB и последовательность выбранного белка.
In [13]:
import sys
sys.path.append('/usr/lib/modeller9v7/modlib/')
sys.path.append('/usr/lib/modeller9v7/lib/x86_64-intel8/python2.5/')
import modeller
import _modeller
import modeller.automodel
In [2]:
env=modeller.environ()
env.io.hetatm=True
MODELLER 9v7, 2009/06/12, r6923
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2009 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, 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 kodomo.fbb.msu.ru 3.8-2-amd64 x86_64
Date and time of compilation : 2009/06/12 12:23:44
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2017/05/26 18:00:33
In [3]:
! wget http://www.pdb.org/pdb/files/1lmp.pdb
--2017-04-21 16:03:58-- http://www.pdb.org/pdb/files/1lmp.pdb
Resolving www.pdb.org... 132.249.231.77
Connecting to www.pdb.org|132.249.231.77|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: http://www.rcsb.org/pdb/files/1lmp.pdb [following]
--2017-04-21 16:03:59-- http://www.rcsb.org/pdb/files/1lmp.pdb
Resolving www.rcsb.org... 132.249.231.10
Connecting to www.rcsb.org|132.249.231.10|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: http://files.rcsb.org/view/1lmp.pdb [following]
--2017-04-21 16:03:59-- http://files.rcsb.org/view/1lmp.pdb
Resolving files.rcsb.org... 132.249.213.140
Connecting to files.rcsb.org|132.249.213.140|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [text/plain]
Saving to: `1lmp.pdb'
[ <=> ] 131,301 158K/s in 0.8s
2017-04-21 16:04:01 (158 KB/s) - `1lmp.pdb' saved [131301]
In [3]:
! wget http://www.uniprot.org/uniprot/LYS_BOMMO.fasta
--2017-05-26 18:00:40-- http://www.uniprot.org/uniprot/LYS_BOMMO.fasta Resolving www.uniprot.org... 193.62.193.81, 128.175.240.211 Connecting to www.uniprot.org|193.62.193.81|:80... connected. HTTP request sent, awaiting response... 302 Found Location: http://www.uniprot.org/uniprot/P48816.fasta [following] --2017-05-26 18:00:41-- http://www.uniprot.org/uniprot/P48816.fasta Reusing existing connection to www.uniprot.org:80. HTTP request sent, awaiting response... 200 OK Length: 195 [text/plain] Saving to: `P48816.fasta' 100%[======================================>] 195 --.-K/s in 0s 2017-05-26 18:00:41 (15.2 MB/s) - `P48816.fasta' saved [195/195]
Построим выравнивание последовательностей лизоцима форели и шелкопряда:
In [5]:
alignm=modeller.alignment(env)
In [6]:
alignm.append(file='LYZ_BOMMO.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 = 'LYZ_aln'
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.
read_pd_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 [7]:
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
Построим модель
In [8]:
## Выбираем объект для моделирования
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()
LYZ_aln 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 target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
88 1 73 76 D C 8.895
END OF TABLE
read_to_681_> topology.submodel read from topology file: 3
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 137
atom names : C +N
atom indices : 1094 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 137
atom names : C CA +N O
atom indices : 1094 1091 0 1095
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: 3
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 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: 11705 10745
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
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 : 137
Number of all, selected real atoms : 1096 1096
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10745 10745
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2205
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 : 896.4709
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 : 1119 0 1 0.008 0.008 23.204 1.000
2 Bond angle potential : 1504 1 7 2.046 2.046 128.04 1.000
3 Stereochemical cosine torsion poten: 713 0 29 47.980 47.980 260.46 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.069 1.069 12.404 1.000
5 Soft-sphere overlap restraints : 2205 0 0 0.002 0.002 1.4087 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) : 2215 0 2 0.311 0.311 97.192 1.000
10 Distance restraints 2 (N-O) : 2371 0 6 0.337 0.337 126.70 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: 136 0 2 4.630 4.630 34.383 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 1 74.885 74.885 30.340 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 61.795 61.795 26.445 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 82.629 82.629 22.599 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 83.776 83.776 14.811 1.000
18 Disulfide distance restraints : 3 0 0 0.023 0.023 0.27485 1.000
19 Disulfide angle restraints : 6 0 0 2.710 2.710 0.97320 1.000
20 Disulfide dihedral angle restraints: 3 0 0 24.594 24.594 1.8101 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) : 1316 0 0 0.343 0.343 25.894 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: 135 17 16 27.770 61.748 65.296 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 0 0.554 0.554 24.233 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: LYZ_aln.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: 14751.1201
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 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2080 88D 88D N CA 697 698 124.70 107.00 17.70 5.09 107.00 17.70 5.09
-------------------------------------------------------------------------------------------------
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 3810 1M 2Q C N 7 9 -78.47 -73.00 9.95 0.75 -63.80 173.32 24.74
1 2Q 2Q N CA 9 10 132.39 140.70 -40.30
2 3811 2Q 3K C N 16 18 58.01 -70.20 143.18 11.70 -62.90 166.91 20.47
2 3K 3K N CA 18 19 -155.87 140.40 -40.80
3 3812 3K 4L C N 25 27 -66.84 -70.70 10.52 0.94 -63.50 167.44 23.44
3 4L 4L N CA 27 28 151.39 141.60 -41.20
4 3815 6I 7F C N 49 51 -94.75 -71.40 25.98 2.12 -63.20 176.45 22.47
4 7F 7F N CA 51 52 129.30 140.70 -44.30
5 3816 7F 8A C N 60 62 -167.81 -134.00 39.34 0.92 -62.50 -175.09 35.87
5 8A 8A N CA 62 63 167.11 147.00 -40.90
6 3817 8A 9L C N 65 67 -104.36 -108.50 12.34 0.70 -63.50 179.39 27.41
6 9L 9L N CA 67 68 144.13 132.50 -41.20
7 3820 11V 12L C N 87 89 -93.83 -70.70 28.14 1.93 -63.50 164.00 24.61
7 12L 12L N CA 89 90 157.63 141.60 -41.20
8 3823 14V 15G C N 108 110 -115.17 -80.20 44.14 3.21 82.20 -146.28 16.58
8 15G 15G N CA 110 111 147.16 174.10 8.50
9 3824 15G 16S C N 112 114 -144.03 -136.60 13.09 0.47 -64.10 -178.43 18.88
9 16S 16S N CA 114 115 161.97 151.20 -35.00
10 3844 35F 36E C N 274 276 56.65 54.60 9.50 0.58 -63.60 140.89 24.25
10 36E 36E N CA 276 277 33.12 42.40 -40.30
11 3860 51S 52S C N 411 413 64.51 56.90 9.51 0.68 -64.10 144.41 19.16
11 52S 52S N CA 413 414 30.69 36.40 -35.00
12 3896 87K 88D C N 695 697 168.59 -96.50 96.43 3.93 -63.30 -172.33 20.93
12 88D 88D N CA 697 698 97.15 114.20 -40.00
13 3920 111I 112Y C N 872 874 -34.49 -98.40 66.92 3.43 -63.50 154.70 26.04
13 112Y 112Y N CA 874 875 108.55 128.40 -43.40
14 3923 114R 115H C N 904 906 -98.32 -125.60 66.86 1.97 -63.20 125.09 13.82
14 115H 115H N CA 906 907 77.76 138.80 -42.30
15 3924 115H 116R C N 914 916 -59.15 -63.00 29.95 3.80 -125.20 162.62 8.89
15 116R 116R N CA 916 917 -70.80 -41.10 140.60
16 3934 125N 126H C N 1010 1012 -120.69 -63.20 71.55 8.58 -63.20 71.55 8.58
16 126H 126H N CA 1012 1013 0.28 -42.30 -42.30
17 3935 126H 127C C N 1020 1022 -121.38 -63.00 58.90 9.38 -63.00 58.90 9.38
17 127C 127C N CA 1022 1023 -33.26 -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 11 12 46 81 116 101 116 142 173 188
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
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 : 137
Number of all, selected real atoms : 1096 1096
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10745 10745
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2221
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 : 895.6688
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 : 1119 0 1 0.008 0.008 22.826 1.000
2 Bond angle potential : 1504 1 7 2.089 2.089 133.64 1.000
3 Stereochemical cosine torsion poten: 713 0 26 47.985 47.985 256.16 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.193 1.193 14.397 1.000
5 Soft-sphere overlap restraints : 2221 0 0 0.002 0.002 1.2234 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) : 2215 0 3 0.306 0.306 98.584 1.000
10 Distance restraints 2 (N-O) : 2371 0 8 0.346 0.346 139.39 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: 136 0 3 4.683 4.683 35.176 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 1 71.447 71.447 25.528 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 73.102 73.102 29.026 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 78.283 78.283 20.915 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 91.710 91.710 12.397 1.000
18 Disulfide distance restraints : 3 0 0 0.026 0.026 0.35156 1.000
19 Disulfide angle restraints : 6 0 0 2.561 2.561 0.86918 1.000
20 Disulfide dihedral angle restraints: 3 0 0 25.887 25.887 1.9748 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) : 1316 0 0 0.288 0.288 18.707 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: 135 18 15 25.297 61.398 62.111 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 0 0.525 0.525 22.395 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: LYZ_aln.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: 14341.2100
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 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2080 88D 88D N CA 697 698 125.84 107.00 18.84 5.42 107.00 18.84 5.42
-------------------------------------------------------------------------------------------------
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 3810 1M 2Q C N 7 9 -124.29 -121.10 20.60 0.92 -63.80 170.73 28.31
1 2Q 2Q N CA 9 10 160.05 139.70 -40.30
2 3812 3K 4L C N 25 27 177.06 -108.50 74.64 3.49 -63.50 -144.67 26.52
2 4L 4L N CA 27 28 137.97 132.50 -41.20
3 3815 6I 7F C N 49 51 -116.60 -124.20 19.24 0.69 -63.20 178.12 21.49
3 7F 7F N CA 51 52 125.63 143.30 -44.30
4 3816 7F 8A C N 60 62 -156.34 -134.00 23.07 0.58 -62.50 -168.97 36.32
4 8A 8A N CA 62 63 152.72 147.00 -40.90
5 3817 8A 9L C N 65 67 -115.14 -108.50 6.79 0.31 -63.50 -177.42 22.96
5 9L 9L N CA 67 68 133.92 132.50 -41.20
6 3823 14V 15G C N 108 110 -73.94 -80.20 14.72 0.34 82.20 -141.90 6.92
6 15G 15G N CA 110 111 160.77 174.10 8.50
7 3824 15G 16S C N 112 114 -79.46 -72.40 14.72 1.10 -64.10 175.16 11.86
7 16S 16S N CA 114 115 139.48 152.40 -35.00
8 3844 35F 36E C N 274 276 55.29 54.60 9.29 0.66 -63.60 139.74 24.05
8 36E 36E N CA 276 277 33.13 42.40 -40.30
9 3859 50E 51S C N 405 407 -143.53 -64.10 92.53 9.12 -64.10 92.53 9.12
9 51S 51S N CA 407 408 12.46 -35.00 -35.00
10 3860 51S 52S C N 411 413 54.13 56.90 3.11 0.27 -64.10 138.85 18.21
10 52S 52S N CA 413 414 37.81 36.40 -35.00
11 3896 87K 88D C N 695 697 -142.04 -63.30 85.62 14.59 -63.30 85.62 14.59
11 88D 88D N CA 697 698 -73.63 -40.00 -40.00
12 3920 111I 112Y C N 872 874 -43.45 -98.40 55.55 2.39 -63.50 164.87 27.19
12 112Y 112Y N CA 874 875 120.24 128.40 -43.40
13 3923 114R 115H C N 904 906 -99.77 -125.60 57.56 1.65 -63.20 134.72 14.93
13 115H 115H N CA 906 907 87.36 138.80 -42.30
14 3924 115H 116R C N 914 916 -59.75 -63.00 27.07 3.45 -125.20 164.97 9.00
14 116R 116R N CA 916 917 -67.97 -41.10 140.60
15 3934 125N 126H C N 1010 1012 -126.21 -63.20 78.52 9.41 -63.20 78.52 9.41
15 126H 126H N CA 1012 1013 4.55 -42.30 -42.30
16 3935 126H 127C C N 1020 1022 -127.91 -63.00 68.14 10.04 -63.00 68.14 10.04
16 127C 127C N CA 1022 1023 -20.37 -41.10 -41.10
17 3936 127C 128Q C N 1026 1028 -57.49 -63.80 21.02 2.80 -121.10 172.13 8.92
17 128Q 128Q N CA 1028 1029 -60.36 -40.30 139.70
18 3937 128Q 129G C N 1035 1037 -74.53 -62.40 13.92 2.13 82.20 162.49 12.16
18 129G 129G N CA 1037 1038 -34.37 -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 7 52 66 104 103 126 148 180 169
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
LYZ_aln.B99990001.pdb 896.47095
LYZ_aln.B99990002.pdb 895.66882
In [9]:
import nglview
import ipywidgets
w1 = nglview.show_structure_file('LYZ_aln.B99990002.pdb')
w1
In [13]:
res_l = []
for res in alignm[0].residues:
res_l.append(res.code)
alignm.append_sequence("".join(res_l+[".", ".", "."]))
In [16]:
alignm[2].code = "LYZ_lig"
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 [17]:
s = alignm[2]
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()
LYZ_lig 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 target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
88 1 73 76 D C 8.895
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 137
atom names : C +N
atom indices : 1094 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 137
atom names : C CA +N O
atom indices : 1094 1091 0 1095
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: 3
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 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: 13094 12134
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
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 : 140
Number of all, selected real atoms : 1139 1139
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12134 12134
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2541
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 : 1241.2863
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 : 1119 0 3 0.010 0.010 29.901 1.000
2 Bond angle potential : 1504 3 14 3.136 3.136 208.00 1.000
3 Stereochemical cosine torsion poten: 713 0 32 48.572 48.572 268.24 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.442 1.442 19.958 1.000
5 Soft-sphere overlap restraints : 2541 1 2 0.008 0.008 17.624 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) : 2215 0 5 0.287 0.287 100.31 1.000
10 Distance restraints 2 (N-O) : 2371 1 17 0.381 0.381 197.69 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: 136 0 5 5.066 5.066 41.163 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 3 83.487 83.487 48.939 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 2 77.352 77.352 50.680 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 68.086 68.086 20.418 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 84.504 84.504 14.269 1.000
18 Disulfide distance restraints : 3 0 0 0.034 0.034 0.59255 1.000
19 Disulfide angle restraints : 6 0 0 5.180 5.180 3.5544 1.000
20 Disulfide dihedral angle restraints: 3 0 0 34.777 34.777 2.2323 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) : 1316 0 0 0.391 0.391 33.369 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: 135 23 22 33.916 67.127 112.61 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 1 0.737 0.737 45.210 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.049 0.049 26.522 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: LYZ_lig.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: 17225.9434
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 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2080 88D 88D N CA 697 698 126.70 107.00 19.70 5.67 107.00 19.70 5.67
-------------------------------------------------------------------------------------------------
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 7531 65S 85P N O 513 683 8.93 6.49 2.44 4.63 6.49 2.44 4.63
-------------------------------------------------------------------------------------------------
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 3810 1M 2Q C N 7 9 -82.10 -73.00 17.28 0.99 -63.80 165.33 25.28
1 2Q 2Q N CA 9 10 155.39 140.70 -40.30
2 3811 2Q 3K C N 16 18 -61.89 -70.20 8.47 0.58 -62.90 179.57 23.37
2 3K 3K N CA 18 19 138.77 140.40 -40.80
3 3812 3K 4L C N 25 27 -107.10 -108.50 12.75 0.70 -63.50 179.01 27.53
3 4L 4L N CA 27 28 145.17 132.50 -41.20
4 3815 6I 7F C N 49 51 -147.17 -124.20 27.33 0.71 -63.20 178.56 30.15
4 7F 7F N CA 51 52 158.12 143.30 -44.30
5 3816 7F 8A C N 60 62 -69.12 -68.20 4.93 0.43 -62.50 178.76 29.62
5 8A 8A N CA 62 63 140.46 145.30 -40.90
6 3817 8A 9L C N 65 67 -105.49 -108.50 29.35 1.55 -63.50 150.48 18.94
6 9L 9L N CA 67 68 103.30 132.50 -41.20
7 3820 11V 12L C N 87 89 -96.06 -108.50 18.61 0.85 -63.50 163.14 21.01
7 12L 12L N CA 89 90 118.66 132.50 -41.20
8 3823 14V 15G C N 108 110 -177.43 -167.20 22.77 0.93 82.20 176.97 12.93
8 15G 15G N CA 110 111 154.26 174.60 8.50
9 3824 15G 16S C N 112 114 -146.10 -136.60 10.07 0.49 -64.10 -164.80 20.00
9 16S 16S N CA 114 115 147.86 151.20 -35.00
10 3844 35F 36E C N 274 276 52.19 54.60 5.83 0.64 -63.60 139.27 23.96
10 36E 36E N CA 276 277 37.08 42.40 -40.30
11 3859 50E 51S C N 405 407 -134.19 -64.10 78.78 8.12 -64.10 78.78 8.12
11 51S 51S N CA 407 408 0.97 -35.00 -35.00
12 3860 51S 52S C N 411 413 58.96 56.90 2.19 0.21 -64.10 141.91 18.71
12 52S 52S N CA 413 414 35.66 36.40 -35.00
13 3893 84S 85P C N 675 677 -45.60 -58.70 60.84 4.07 -64.50 124.34 10.30
13 85P 85P N CA 677 678 -89.91 -30.50 147.20
14 3894 85P 86G C N 682 684 -66.47 -62.40 16.35 2.66 82.20 162.48 12.55
14 86G 86G N CA 684 685 -57.04 -41.20 8.50
15 3895 86G 87K C N 686 688 68.53 -70.20 138.81 10.24 -70.20 138.81 10.24
15 87K 87K N CA 688 689 144.97 140.40 140.40
16 3896 87K 88D C N 695 697 -154.82 -63.30 97.62 16.57 -63.30 97.62 16.57
16 88D 88D N CA 697 698 -73.96 -40.00 -40.00
17 3898 89C 90N C N 709 711 168.38 -63.20 128.54 19.71 55.90 141.59 9.77
17 90N 90N N CA 711 712 -46.51 -41.10 39.50
18 3920 111I 112Y C N 872 874 -46.67 -98.40 53.80 2.69 -63.50 157.92 25.92
18 112Y 112Y N CA 874 875 113.62 128.40 -43.40
19 3922 113K 114R C N 893 895 -80.15 -125.20 81.45 2.77 -63.00 115.12 14.47
19 114R 114R N CA 895 896 72.74 140.60 -41.10
20 3923 114R 115H C N 904 906 -163.47 -63.20 100.30 15.80 -63.20 100.30 15.80
20 115H 115H N CA 906 907 -40.00 -42.30 -42.30
21 3935 126H 127C C N 1020 1022 -129.90 -63.00 84.35 10.29 -63.00 84.35 10.29
21 127C 127C N CA 1022 1023 10.29 -41.10 -41.10
22 3936 127C 128Q C N 1026 1028 -58.29 -63.80 23.03 3.12 -121.10 169.68 8.80
22 128Q 128Q N CA 1028 1029 -62.67 -40.30 139.70
23 3937 128Q 129G C N 1035 1037 -76.74 -62.40 16.32 2.51 82.20 164.38 12.27
23 129G 129G N CA 1037 1038 -33.42 -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 14 18 67 85 133 123 140 171 190 197
<< end of ENERGY.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
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 : 140
Number of all, selected real atoms : 1139 1139
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12134 12134
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2336
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 : 1028.7402
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 : 1119 0 2 0.009 0.009 28.554 1.000
2 Bond angle potential : 1504 1 7 2.264 2.264 153.32 1.000
3 Stereochemical cosine torsion poten: 713 0 28 48.589 48.589 267.64 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.330 1.330 18.136 1.000
5 Soft-sphere overlap restraints : 2336 1 2 0.008 0.008 16.635 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) : 2215 0 5 0.297 0.297 103.20 1.000
10 Distance restraints 2 (N-O) : 2371 0 9 0.326 0.326 137.48 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: 136 0 2 4.326 4.326 30.018 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 3 77.190 77.190 37.942 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 67.811 67.811 36.506 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 75.344 75.344 22.613 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 77.045 77.045 12.729 1.000
18 Disulfide distance restraints : 3 0 0 0.025 0.025 0.32177 1.000
19 Disulfide angle restraints : 6 0 0 2.340 2.340 0.72531 1.000
20 Disulfide dihedral angle restraints: 3 0 0 25.897 25.897 1.9982 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) : 1316 0 0 0.370 0.370 30.929 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: 135 15 13 28.355 60.370 69.117 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 1 0.614 0.614 29.548 1.000
27 Distance restraints 5 (X-Y) : 1389 0 3 0.053 0.053 31.325 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: LYZ_lig.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: 15770.6992
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 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2080 88D 88D N CA 697 698 128.30 107.00 21.30 6.12 107.00 21.30 6.12
-------------------------------------------------------------------------------------------------
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 3810 1M 2Q C N 7 9 -77.42 -73.00 9.65 0.56 -63.80 170.96 25.86
1 2Q 2Q N CA 9 10 149.28 140.70 -40.30
2 3811 2Q 3K C N 16 18 -107.13 -118.00 15.48 0.55 -62.90 174.58 20.68
2 3K 3K N CA 18 19 128.08 139.10 -40.80
3 3812 3K 4L C N 25 27 -99.54 -108.50 10.42 0.56 -63.50 -177.38 23.54
3 4L 4L N CA 27 28 137.83 132.50 -41.20
4 3815 6I 7F C N 49 51 -107.53 -124.20 23.21 0.62 -63.20 177.09 21.82
4 7F 7F N CA 51 52 127.15 143.30 -44.30
5 3816 7F 8A C N 60 62 -140.33 -134.00 15.62 0.69 -62.50 175.97 33.01
5 8A 8A N CA 62 63 161.27 147.00 -40.90
6 3817 8A 9L C N 65 67 -107.05 -108.50 12.19 0.67 -63.50 179.56 27.60
6 9L 9L N CA 67 68 144.60 132.50 -41.20
7 3820 11V 12L C N 87 89 -139.20 -108.50 41.43 1.85 -63.50 175.62 29.07
7 12L 12L N CA 89 90 160.33 132.50 -41.20
8 3823 14V 15G C N 108 110 68.79 78.70 10.70 0.60 82.20 179.13 9.37
8 15G 15G N CA 110 111 -170.12 -166.10 8.50
9 3824 15G 16S C N 112 114 -124.03 -136.60 15.42 0.47 -64.10 -172.87 11.53
9 16S 16S N CA 114 115 142.27 151.20 -35.00
10 3844 35F 36E C N 274 276 53.24 54.60 7.69 0.70 -63.60 138.91 23.90
10 36E 36E N CA 276 277 34.83 42.40 -40.30
11 3860 51S 52S C N 411 413 63.88 56.90 10.17 0.58 -64.10 143.10 19.01
11 52S 52S N CA 413 414 29.01 36.40 -35.00
12 3896 87K 88D C N 695 697 174.37 -96.50 93.98 3.82 -63.30 174.48 19.64
12 88D 88D N CA 697 698 84.42 114.20 -40.00
13 3920 111I 112Y C N 872 874 -47.28 -98.40 56.68 3.45 -63.50 148.21 24.35
13 112Y 112Y N CA 874 875 103.92 128.40 -43.40
14 3934 125N 126H C N 1010 1012 -123.28 -63.20 78.90 9.17 -63.20 78.90 9.17
14 126H 126H N CA 1012 1013 8.83 -42.30 -42.30
15 3935 126H 127C C N 1020 1022 -124.98 -63.00 62.75 9.90 -63.00 62.75 9.90
15 127C 127C N CA 1022 1023 -31.30 -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 7 15 53 88 104 105 123 154 183 179
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
LYZ_lig.B99990001.pdb 1241.28625
LYZ_lig.B99990002.pdb 1028.74023
In [11]:
import nglview
import ipywidgets
w1 = nglview.show_structure_file('LYZ_lig.B99990001.pdb')
w1
Посмотрим на полученные структуры. Modeller выдал два варианта, они показаны голубым и фиолетовым. Исходная структура лизоцима форели показана жёлтым. В целом, модели похожи по расположению вторичной структуры, но не идентичны друг другу. У исходной структуры нет такого длинного N-хвоста.
In [14]:
from IPython.display import Image
Image(filename='pr10.png')
Out[14]:
Далее была попытка перем естить лиганд в другое место, но ... ничего не вышло
In [12]:
class mymodel(modeller.automodel.automodel):
def special_restraints(self, aln):
rsr = self.restraints
for ids in (('CB:137', 'O6:139'),
('SG:137', 'O6:139'),
('CA:137', 'C1:139')):
atoms = [self.atoms[i] for i in ids]
# rsr.add(forms.upper_bound(group=physical.upper_distance,
# feature=features.distance(*atoms), mean=3.5, stdev=0.1))
a = mymodel(env, alnfile='all_in_one.ali', knowns= pdb.code , sequence = 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 target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
88 1 73 76 D C 8.895
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 137
atom names : C +N
atom indices : 1094 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 137
atom names : C CA +N O
atom indices : 1094 1091 0 1095
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: 3
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 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
--------------------------------------------------------------------------- KeyError Traceback (most recent call last) <ipython-input-12-a0ec74e2eb90> in <module>() 11 a.starting_model = 1 12 a.ending_model = 2 ---> 13 a.make() /usr/lib/modeller9v7/modlib/modeller/automodel/automodel.py in make(self, exit_stage) 96 97 self.outputs = [] ---> 98 self.homcsr(exit_stage) 99 # Exit early? 100 if exit_stage >= 1: /usr/lib/modeller9v7/modlib/modeller/automodel/automodel.py in homcsr(self, exit_stage) 433 # make and write the stereochemical, homology, and special restraints? 434 if self.create_restraints: --> 435 self.mkhomcsr(selection(self), aln) 436 self.restraints.condense() 437 self.restraints.write(self.csrfile) /usr/lib/modeller9v7/modlib/modeller/automodel/automodel.py in mkhomcsr(self, atmsel, aln) 521 # Special restraints have to be called last so that possible cis-proline 522 # changes are reflected in the current restraints: --> 523 self.special_restraints(aln) 524 525 def distance_restraints(self, atmsel, aln): <ipython-input-12-a0ec74e2eb90> in special_restraints(self, aln) 5 ('SG:137', 'O6:139'), 6 ('CA:137', 'C1:139')): ----> 7 atoms = [self.atoms[i] for i in ids] 8 # rsr.add(forms.upper_bound(group=physical.upper_distance, 9 # feature=features.distance(*atoms), mean=3.5, stdev=0.1)) /usr/lib/modeller9v7/modlib/modeller/coordinates.py in __getitem__(self, indx) 359 def __getitem__(self, indx): 360 ret = modutil.handle_seq_indx(self, indx, self.mdl._indxatm, --> 361 (self.offset, self.length, self.suffix)) 362 if isinstance(ret, int): 363 return self.mdl._atom_class(self.mdl, ret + self.offset) /usr/lib/modeller9v7/modlib/modeller/util/modutil.py in handle_seq_indx(seqtype, indx, lookup_func, lookup_args, require_inrange) 17 elif lookup_func is not None: 18 args = lookup_args + (indx,) ---> 19 int_indx = lookup_func(*args) 20 if int_indx < 0: 21 raise KeyError(indx) /usr/lib/modeller9v7/modlib/modeller/coordinates.py in _indxatm(self, offset, length, suffix, indx) 272 newindx = func(self.cdpt, self.seqpt, indx+suffix) - 1 - offset 273 if newindx < 0 or (length is not None and newindx >= length): --> 274 raise KeyError("No such atom: %s" % indx) 275 return newindx 276 raise TypeError("Atom IDs must be numbers or strings") KeyError: 'No such atom: O6:139'
In [33]:
import nglview
import ipywidgets
w1 = nglview.show_structure_file('LYZ_lig.B99990002.pdb')
w1