Гомологичное моделирование комплекса белка с лигандом¶
Цель занятия - ознакомиться с возможностями гомологичного моделирования комплекса белка с лигандом. В этом занятии мы будем пользоваться пакетом Modeller. Это программное обеспечение распространяется бесплатно для академических пользователей. Используя известную структуру лизоцима форели как образец, построим модель комплекса белка лизоцима дальневосточной жабы LYS_BUFAN с лигандом. Скачаем заготовку из PDB и последовательность выбранного белка.
In [2]:
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 [4]:
env=modeller.environ()
env.io.hetatm=True
In [8]:
! wget http://www.pdb.org/pdb/files/1lmp.pdb
--2017-04-21 15:59:56-- 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 15:59:57-- 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 15:59:57-- 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.2'
[ <=> ] 131,301 160K/s in 0.8s
2017-04-21 15:59:58 (160 KB/s) - `1lmp.pdb.2' saved [131301]
In [9]:
! wget http://www.uniprot.org/uniprot/LYS_BUFAN.fasta
--2017-04-21 16:01:48-- http://www.uniprot.org/uniprot/LYS_BUFAN.fasta Resolving www.uniprot.org... 128.175.240.211, 193.62.193.81 Connecting to www.uniprot.org|128.175.240.211|:80... connected. HTTP request sent, awaiting response... 302 Found Location: /uniprot/P85045.fasta [following] --2017-04-21 16:01:48-- http://www.uniprot.org/uniprot/P85045.fasta Reusing existing connection to www.uniprot.org:80. HTTP request sent, awaiting response... 200 OK Length: 231 [text/plain] Saving to: `P85045.fasta' 100%[======================================>] 231 --.-K/s in 0s 2017-04-21 16:01:48 (23.0 MB/s) - `P85045.fasta' saved [231/231]
Построим выравнивание последовательностей лизоцима форели и жабы:
In [43]:
alignm=modeller.alignment(env)
In [44]:
alignm.append(file='P85045.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')
## есть смысл поправить идентификаторы, это будет в дальнейшем в названии файлов
alignm[0].code = 'P85045'
In [25]:
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 [26]:
## 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()
P85045 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
----------------------------------------------
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 10 146
atom names : C +N
atom indices : 1164 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 10 146
atom names : C CA +N O
atom indices : 1164 1159 0 1165
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 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: 13044 12008
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 : 146
Number of all, selected real atoms : 1166 1166
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12008 12008
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2321
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 : 858.3019
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 : 1197 0 0 0.006 0.006 11.523 1.000
2 Bond angle potential : 1618 0 7 2.212 2.212 155.27 1.000
3 Stereochemical cosine torsion poten: 814 0 28 47.325 47.325 275.94 1.000
4 Stereochemical improper torsion pot: 502 0 0 1.200 1.200 17.155 1.000
5 Soft-sphere overlap restraints : 2321 0 0 0.002 0.002 0.65122 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 0.128 0.128 37.057 1.000
10 Distance restraints 2 (N-O) : 2564 0 3 0.181 0.181 85.178 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: 145 0 3 4.627 4.627 36.614 1.000
14 Sidechain Chi_1 dihedral restraints: 126 0 1 66.549 66.549 19.757 1.000
15 Sidechain Chi_2 dihedral restraints: 93 0 0 70.362 70.362 33.787 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 79.567 79.567 23.557 1.000
17 Sidechain Chi_4 dihedral restraints: 21 0 0 78.775 78.775 13.961 1.000
18 Disulfide distance restraints : 4 0 0 0.009 0.009 0.50379E-01 1.000
19 Disulfide angle restraints : 8 0 0 1.714 1.714 0.51906 1.000
20 Disulfide dihedral angle restraints: 4 0 0 31.405 31.405 3.4443 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) : 1582 0 0 0.467 0.467 47.536 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: 144 16 13 20.695 58.989 27.991 1.000
26 Distance restraints 4 (SDCH-SDCH) : 744 0 0 0.750 0.750 68.305 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: P85045.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: 14591.1025
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 4148 1S 2G C N 5 7 -145.44 -167.20 36.17 0.94 82.20 -169.36 14.57
1 2G 2G N CA 7 8 145.70 174.60 8.50
2 4149 2G 3K C N 9 11 -102.04 -118.00 31.19 1.23 -62.90 158.03 18.75
2 3K 3K N CA 11 12 112.30 139.10 -40.80
3 4150 3K 4Y C N 18 20 -120.43 -124.30 6.28 0.26 -63.50 -177.06 26.39
3 4Y 4Y N CA 20 21 130.45 135.40 -43.40
4 4152 5I 6S C N 38 40 -123.74 -136.60 15.01 0.79 -64.10 176.43 16.98
4 6S 6S N CA 40 41 158.95 151.20 -35.00
5 4153 6S 7W C N 44 46 -73.46 -71.30 11.34 0.80 -63.00 166.00 21.40
5 7W 7W N CA 46 47 150.13 139.00 -44.20
6 4154 7W 8E C N 58 60 -104.10 -117.80 18.91 0.60 -63.60 168.99 20.58
6 8E 8E N CA 60 61 123.77 136.80 -40.30
7 4155 8E 9D C N 67 69 -122.33 -96.50 40.49 1.67 -63.30 136.45 14.50
7 9D 9D N CA 69 70 83.03 114.20 -40.00
8 4156 9D 10S C N 75 77 -109.99 -136.60 27.32 0.93 -64.10 -174.26 11.57
8 10S 10S N CA 77 78 144.98 151.20 -35.00
9 4159 12S 13Y C N 93 95 -66.75 -98.40 32.35 1.34 -63.50 178.54 28.16
9 13Y 13Y N CA 95 96 135.10 128.40 -43.40
10 4160 13Y 14L C N 105 107 -71.26 -70.70 10.67 0.79 -63.50 166.72 23.60
10 14L 14L N CA 107 108 152.26 141.60 -41.20
11 4162 15Q 16L C N 122 124 -71.85 -70.70 1.79 0.18 -63.50 178.76 25.31
11 16L 16L N CA 124 125 140.23 141.60 -41.20
12 4163 16L 17Q C N 130 132 -118.04 -121.10 14.46 0.63 -63.80 174.51 23.20
12 17Q 17Q N CA 132 133 125.57 139.70 -40.30
13 4198 51E 52S C N 414 416 -137.70 -64.10 81.56 8.56 -64.10 81.56 8.56
13 52S 52S N CA 416 417 0.16 -35.00 -35.00
14 4210 63P 64P C N 504 506 -75.49 -58.70 17.64 1.90 -64.50 172.63 13.47
14 64P 64P N CA 506 507 -25.08 -30.50 147.20
15 4279 132C 133K C N 1054 1056 -51.61 -62.90 28.44 3.28 -70.20 153.83 11.57
15 133K 133K N CA 1056 1057 -66.90 -40.80 140.40
16 4280 133K 134G C N 1063 1065 -75.00 -62.40 15.35 2.28 82.20 162.45 12.12
16 134G 134G N CA 1065 1066 -32.45 -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 7 5 40 66 121 114 135 154 167 190
<< 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 : 146
Number of all, selected real atoms : 1166 1166
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12008 12008
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2416
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 : 785.2393
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 : 1197 0 0 0.006 0.006 11.297 1.000
2 Bond angle potential : 1618 0 6 2.082 2.082 140.40 1.000
3 Stereochemical cosine torsion poten: 814 0 30 47.211 47.211 281.54 1.000
4 Stereochemical improper torsion pot: 502 0 0 1.212 1.212 17.209 1.000
5 Soft-sphere overlap restraints : 2416 0 0 0.001 0.001 0.50072 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 0.123 0.123 33.800 1.000
10 Distance restraints 2 (N-O) : 2564 0 0 0.161 0.161 69.693 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: 145 0 2 4.243 4.243 30.783 1.000
14 Sidechain Chi_1 dihedral restraints: 126 0 0 63.073 63.073 14.516 1.000
15 Sidechain Chi_2 dihedral restraints: 93 0 0 71.196 71.196 36.508 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 78.144 78.144 25.899 1.000
17 Sidechain Chi_4 dihedral restraints: 21 0 0 77.065 77.065 14.328 1.000
18 Disulfide distance restraints : 4 0 0 0.008 0.008 0.41944E-01 1.000
19 Disulfide angle restraints : 8 0 0 1.838 1.838 0.59700 1.000
20 Disulfide dihedral angle restraints: 4 0 0 29.519 29.519 3.3655 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) : 1582 0 0 0.338 0.338 24.598 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: 144 16 13 24.038 61.228 45.027 1.000
26 Distance restraints 4 (SDCH-SDCH) : 744 0 0 0.543 0.543 35.141 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: P85045.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: 14358.1240
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 4149 2G 3K C N 9 11 -65.71 -70.20 5.84 0.49 -62.90 175.09 22.89
1 3K 3K N CA 11 12 144.13 140.40 -40.80
2 4150 3K 4Y C N 18 20 -71.95 -98.40 26.59 1.03 -63.50 174.81 27.31
2 4Y 4Y N CA 20 21 131.21 128.40 -43.40
3 4152 5I 6S C N 38 40 -147.84 -136.60 21.52 0.80 -64.10 176.57 18.81
3 6S 6S N CA 40 41 169.55 151.20 -35.00
4 4153 6S 7W C N 44 46 -64.89 -71.30 16.88 1.10 -63.00 167.59 20.84
4 7W 7W N CA 46 47 123.38 139.00 -44.20
5 4154 7W 8E C N 58 60 -126.80 -117.80 9.06 0.31 -63.60 -170.98 22.39
5 8E 8E N CA 60 61 137.84 136.80 -40.30
6 4156 9D 10S C N 75 77 -127.64 -136.60 11.71 0.37 -64.10 -170.38 11.68
6 10S 10S N CA 77 78 143.66 151.20 -35.00
7 4158 11C 12S C N 87 89 -125.13 -136.60 13.35 0.70 -64.10 177.76 17.18
7 12S 12S N CA 89 90 158.04 151.20 -35.00
8 4159 12S 13Y C N 93 95 -115.28 -124.30 10.01 0.58 -63.50 -178.02 26.44
8 13Y 13Y N CA 95 96 131.06 135.40 -43.40
9 4160 13Y 14L C N 105 107 -120.89 -108.50 12.39 0.59 -63.50 -176.88 22.86
9 14L 14L N CA 107 108 132.69 132.50 -41.20
10 4161 14L 15Q C N 113 115 -136.54 -121.10 25.01 0.86 -63.80 176.05 29.70
10 15Q 15Q N CA 115 116 159.38 139.70 -40.30
11 4162 15Q 16L C N 122 124 -110.82 -108.50 60.53 3.25 -63.50 134.41 21.59
11 16L 16L N CA 124 125 -167.01 132.50 -41.20
12 4163 16L 17Q C N 130 132 -74.09 -73.00 15.51 1.04 -63.80 165.85 23.86
12 17Q 17Q N CA 132 133 125.23 140.70 -40.30
13 4198 51E 52S C N 414 416 -137.53 -64.10 81.39 8.55 -64.10 81.39 8.55
13 52S 52S N CA 416 417 0.09 -35.00 -35.00
14 4210 63P 64P C N 504 506 -60.58 -58.70 7.21 0.75 -64.50 175.38 13.29
14 64P 64P N CA 506 507 -37.46 -30.50 147.20
15 4265 118D 119P C N 942 944 -68.86 -64.50 31.70 2.60 -58.70 146.65 11.31
15 119P 119P N CA 944 945 115.80 147.20 -30.50
16 4266 119P 120N C N 949 951 147.79 -63.20 149.02 22.65 -63.20 149.02 22.65
16 120N 120N N CA 951 952 -42.82 -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 6 10 44 72 115 105 131 172 172 178
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
P85045.B99990001.pdb 858.30188
P85045.B99990002.pdb 785.23926
In [51]:
import nglview
import ipywidgets
w1 = nglview.show_structure_file('P85045.B99990001.pdb')
w1
In [38]:
## Получим список остатков последовательности
new_list = []
for smth in alignm[0].residues:
new_list.append(smth.code)
for i in range(3): new_list.append('.') #для того чтобы взять из PDB файла лизоцима форели три последние компоненты, это лиганды
new_line = ''.join(new_list)
print new_line
SGKYISWEDSCSYLQLQKYERCELAKALKKGGLADFKGYSLENWICTAFHESGYNTASTNYNPPDKSTDYGIFQINSRWWCNDYKTPRSKNTCNIDCKVLLGDDISPAIKCAKRVVSDPNGMGAWVAWKKYCKGKNLSQWTQGCKL...
In [45]:
## Добавим в объект выравнивание последовательность из строки
alignm.append_sequence(new_line)
In [49]:
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 [50]:
## Выбираем объект для моделирования
new = alignm[2]
pdb = alignm[1]
new.code = 'new'
print s.code, pdb.code,new.code
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='all_in_one.ali', knowns= pdb.code, sequence = new.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
P85045 1lmp new
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
----------------------------------------------
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 10 146
atom names : C +N
atom indices : 1164 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 10 146
atom names : C CA +N O
atom indices : 1164 1159 0 1165
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 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: 14445 13409
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 : 149
Number of all, selected real atoms : 1209 1209
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13409 13409
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2599
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 : 969.0060
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 : 1197 0 0 0.006 0.006 12.273 1.000
2 Bond angle potential : 1618 0 10 2.264 2.264 162.67 1.000
3 Stereochemical cosine torsion poten: 814 0 30 47.154 47.154 279.56 1.000
4 Stereochemical improper torsion pot: 502 0 0 1.283 1.283 19.695 1.000
5 Soft-sphere overlap restraints : 2599 1 2 0.007 0.007 14.675 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 0.130 0.130 41.421 1.000
10 Distance restraints 2 (N-O) : 2564 1 9 0.222 0.222 125.58 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: 145 0 3 4.732 4.732 38.287 1.000
14 Sidechain Chi_1 dihedral restraints: 126 0 0 69.971 69.971 25.813 1.000
15 Sidechain Chi_2 dihedral restraints: 93 0 1 74.817 74.817 35.850 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 71.814 71.814 24.115 1.000
17 Sidechain Chi_4 dihedral restraints: 21 0 0 88.784 88.784 15.781 1.000
18 Disulfide distance restraints : 4 0 0 0.008 0.008 0.45310E-01 1.000
19 Disulfide angle restraints : 8 0 0 1.508 1.508 0.40162 1.000
20 Disulfide dihedral angle restraints: 4 0 0 35.824 35.824 4.3226 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) : 1582 0 0 0.424 0.424 46.151 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: 144 18 15 21.963 64.140 49.894 1.000
26 Distance restraints 4 (SDCH-SDCH) : 744 0 1 0.682 0.682 57.136 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.036 0.036 15.324 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: new.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: 16123.2061
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 8128 67S 87P N O 530 712 8.56 6.49 2.07 4.55 6.49 2.07 4.55
-------------------------------------------------------------------------------------------------
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 4149 2G 3K C N 9 11 -70.86 -70.20 16.51 1.21 -62.90 164.89 20.99
1 3K 3K N CA 11 12 123.90 140.40 -40.80
2 4150 3K 4Y C N 18 20 -133.49 -124.30 14.74 0.61 -63.50 -176.45 32.61
2 4Y 4Y N CA 20 21 146.92 135.40 -43.40
3 4152 5I 6S C N 38 40 -81.68 -72.40 9.43 0.62 -64.10 171.83 13.57
3 6S 6S N CA 40 41 154.07 152.40 -35.00
4 4153 6S 7W C N 44 46 -82.42 -71.30 14.73 0.86 -63.00 168.28 22.27
4 7W 7W N CA 46 47 148.65 139.00 -44.20
5 4154 7W 8E C N 58 60 -115.91 -117.80 5.08 0.28 -63.60 -174.30 27.72
5 8E 8E N CA 60 61 141.51 136.80 -40.30
6 4155 8E 9D C N 67 69 -79.93 -96.50 24.42 1.02 -63.30 137.27 16.00
6 9D 9D N CA 69 70 96.26 114.20 -40.00
7 4156 9D 10S C N 75 77 -164.69 -136.60 47.09 1.65 -64.10 169.16 19.52
7 10S 10S N CA 77 78 -171.01 151.20 -35.00
8 4158 11C 12S C N 87 89 -63.26 -72.40 34.25 1.72 -64.10 154.40 11.24
8 12S 12S N CA 89 90 119.40 152.40 -35.00
9 4159 12S 13Y C N 93 95 171.84 -124.30 67.82 5.58 -63.50 -160.33 27.55
9 13Y 13Y N CA 95 96 112.58 135.40 -43.40
10 4160 13Y 14L C N 105 107 -143.45 -108.50 36.78 1.90 -63.50 -179.13 22.17
10 14L 14L N CA 107 108 121.04 132.50 -41.20
11 4161 14L 15Q C N 113 115 -160.00 -121.10 46.51 1.44 -63.80 -177.98 31.65
11 15Q 15Q N CA 115 116 165.18 139.70 -40.30
12 4162 15Q 16L C N 122 124 -73.61 -70.70 15.31 1.05 -63.50 162.48 23.15
12 16L 16L N CA 124 125 156.63 141.60 -41.20
13 4163 16L 17Q C N 130 132 -85.56 -73.00 36.70 2.65 -63.80 148.13 20.70
13 17Q 17Q N CA 132 133 106.22 140.70 -40.30
14 4210 63P 64P C N 504 506 -79.23 -58.70 22.84 2.21 -64.50 168.34 13.35
14 64P 64P N CA 506 507 -20.50 -30.50 147.20
15 4233 86T 87P C N 704 706 -46.16 -58.70 65.60 4.48 -64.50 119.33 9.90
15 87P 87P N CA 706 707 -94.88 -30.50 147.20
16 4234 87P 88R C N 711 713 -96.14 -72.10 61.35 5.17 57.30 160.61 16.10
16 88R 88R N CA 713 714 85.46 141.90 38.00
17 4279 132C 133K C N 1054 1056 -53.42 -62.90 23.51 2.71 -70.20 158.18 11.85
17 133K 133K N CA 1056 1057 -62.31 -40.80 140.40
18 4280 133K 134G C N 1063 1065 -76.28 -62.40 16.36 2.47 82.20 163.71 12.20
18 134G 134G N CA 1065 1066 -32.54 -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 10 10 60 69 126 127 133 196 187 216
<< 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.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 149
Number of all, selected real atoms : 1209 1209
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13409 13409
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2685
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 : 884.0015
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 : 1197 0 0 0.007 0.007 14.555 1.000
2 Bond angle potential : 1618 0 6 2.247 2.247 161.49 1.000
3 Stereochemical cosine torsion poten: 814 0 27 47.045 47.045 281.24 1.000
4 Stereochemical improper torsion pot: 502 0 0 1.343 1.343 20.558 1.000
5 Soft-sphere overlap restraints : 2685 1 2 0.007 0.007 15.483 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 0.115 0.115 35.418 1.000
10 Distance restraints 2 (N-O) : 2564 0 0 0.165 0.165 68.996 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: 145 0 3 4.442 4.442 33.746 1.000
14 Sidechain Chi_1 dihedral restraints: 126 0 0 72.386 72.386 34.576 1.000
15 Sidechain Chi_2 dihedral restraints: 93 0 1 80.100 80.100 36.854 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 82.833 82.833 26.335 1.000
17 Sidechain Chi_4 dihedral restraints: 21 0 0 82.092 82.092 14.398 1.000
18 Disulfide distance restraints : 4 0 0 0.010 0.010 0.73453E-01 1.000
19 Disulfide angle restraints : 8 0 0 2.723 2.723 1.3097 1.000
20 Disulfide dihedral angle restraints: 4 0 0 28.948 28.948 2.9157 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) : 1582 0 0 0.409 0.409 41.414 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: 144 17 13 20.373 61.039 36.378 1.000
26 Distance restraints 4 (SDCH-SDCH) : 744 0 0 0.637 0.637 44.094 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.034 0.034 14.167 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: new.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: 16238.7637
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 4148 1S 2G C N 5 7 -167.54 -167.20 4.84 0.19 82.20 -164.65 14.25
1 2G 2G N CA 7 8 169.77 174.60 8.50
2 4149 2G 3K C N 9 11 -66.09 -70.20 4.12 0.31 -62.90 178.55 23.36
2 3K 3K N CA 11 12 140.68 140.40 -40.80
3 4150 3K 4Y C N 18 20 -124.68 -124.30 5.95 0.30 -63.50 -174.37 32.54
3 4Y 4Y N CA 20 21 141.34 135.40 -43.40
4 4152 5I 6S C N 38 40 -140.35 -136.60 4.41 0.13 -64.10 -172.33 19.03
4 6S 6S N CA 40 41 153.52 151.20 -35.00
5 4153 6S 7W C N 44 46 -71.05 -71.30 6.26 0.47 -63.00 177.13 21.68
5 7W 7W N CA 46 47 132.75 139.00 -44.20
6 4154 7W 8E C N 58 60 -105.85 -117.80 18.66 1.01 -63.60 173.78 25.56
6 8E 8E N CA 60 61 151.13 136.80 -40.30
7 4155 8E 9D C N 67 69 -72.99 -70.90 11.05 0.45 -63.30 159.15 20.24
7 9D 9D N CA 69 70 161.15 150.30 -40.00
8 4156 9D 10S C N 75 77 -60.30 -72.40 14.20 0.76 -64.10 -180.00 13.27
8 10S 10S N CA 77 78 144.96 152.40 -35.00
9 4158 11C 12S C N 87 89 -85.18 -72.40 19.78 0.91 -64.10 158.89 12.88
9 12S 12S N CA 89 90 167.51 152.40 -35.00
10 4159 12S 13Y C N 93 95 -91.81 -98.40 6.60 0.26 -63.50 173.84 26.18
10 13Y 13Y N CA 95 96 128.12 128.40 -43.40
11 4160 13Y 14L C N 105 107 -89.07 -108.50 20.86 0.93 -63.50 168.07 22.00
11 14L 14L N CA 107 108 124.92 132.50 -41.20
12 4161 14L 15Q C N 113 115 -135.22 -121.10 31.11 1.19 -63.80 168.19 28.46
12 15Q 15Q N CA 115 116 167.43 139.70 -40.30
13 4162 15Q 16L C N 122 124 -106.75 -108.50 9.64 0.50 -63.50 169.82 21.51
13 16L 16L N CA 124 125 123.02 132.50 -41.20
14 4163 16L 17Q C N 130 132 -145.18 -121.10 28.47 0.88 -63.80 -176.20 31.26
14 17Q 17Q N CA 132 133 154.90 139.70 -40.30
15 4198 51E 52S C N 414 416 -138.92 -64.10 85.07 8.64 -64.10 85.07 8.64
15 52S 52S N CA 416 417 5.48 -35.00 -35.00
16 4209 62N 63P C N 497 499 -67.70 -64.50 67.75 4.89 -58.70 114.98 10.24
16 63P 63P N CA 499 500 -145.13 147.20 -30.50
17 4210 63P 64P C N 504 506 -57.47 -58.70 24.52 2.13 -64.50 153.36 11.08
17 64P 64P N CA 506 507 -6.00 -30.50 147.20
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 4 12 45 83 130 135 167 159 211 205
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
new.B99990001.pdb 969.00598
new.B99990002.pdb 884.00146
In [53]:
import nglview
import ipywidgets
w1 = nglview.show_structure_file('new.B99990001.pdb')
w1
Посмотрим на полученные структуры. Modeller выдал два варианта, они показаны розовым и голубым. Исходная структура лизоцима форели показана фиолетовым. В целом, модели похожи по расположению вторичной структуры, но не идентичны друг другу. У исходной структуры нет такого длинного хвоста.
In [1]:
import nglview
import ipywidgets
w1 = nglview.show_structure_file('new.B99990001.pdb')
w1
In [1]:
from IPython.display import Image
Image(filename='pr10.png')
Out[1]:
Попробуем присоединить лиганд в другое место. Так как лиганд с точки зрения Modeller - твердое тело, то достаточно указать 3 точки в пространстве, куда ему нужно присоединиться. Попробую присоединить на N-конец. Что-то он пока не работает. В процессе доработки. Номера атомов соответствуют PDB файлу.
In [64]:
class mymodel(modeller.automodel.automodel):
def special_restraints(self, aln):
rsr = self.restraints
for ids in (('CA:1', 'O6:147'),
('N:2', 'O6:148'),
('CA:2', 'C1:149')):
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 = new.code)
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
----------------------------------------------
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 10 146
atom names : C +N
atom indices : 1164 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 10 146
atom names : C CA +N O
atom indices : 1164 1159 0 1165
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 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
indxatm_278E> No ":" in ATOM:RESID[:CHAINID] atom identifier: C
--------------------------------------------------------------------------- ModellerError Traceback (most recent call last) <ipython-input-64-19d6e6e80947> in <module>() 7 # feature=features.distance(*atoms), mean=3.5, stdev=0.1)) 8 a = mymodel(env, alnfile='all_in_one.ali', knowns= pdb.code, sequence = new.code) ----> 9 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-64-19d6e6e80947> in special_restraints(self, aln) 3 rsr = self.restraints 4 for ids in (('CA:1', 'O6:147')): ----> 5 atoms = [self.atoms[i] for i in ids] 6 # rsr.add(forms.upper_bound(group=physical.upper_distance, 7 # 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) 270 if isinstance(indx, str): 271 func = _modeller.mod_coordinates_find_atom --> 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) ModellerError: indxatm_278E> No ":" in ATOM:RESID[:CHAINID] atom identifier: C