8. Гомологичное моделирование комплекса белка с лигандом¶
In [1]:
import sys
In [2]:
#conda install -c salilab modeller
In [3]:
import modeller
import _modeller
import modeller.automodel
In [4]:
env=modeller.environ()
env.io.hetatm=True
MODELLER 9.21, 2018/12/06, r11301
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2018 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Darwin mbp-marina 18.5.0 x86_64
Date and time of compilation : 2018/12/06 10:04:19
MODELLER executable type : mac10v4-intel64
Job starting time (YY/MM/DD HH:MM:SS): 2019/05/30 08:25:01
In [5]:
alignm=modeller.alignment(env)
In [6]:
#добавим последовательность и структуру
alignm.append(file='P05105.2.fasta', align_codes='all',alignment_format='FASTA')
#создадим модель
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
#и добавим в выравнивание
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
read_pd_459W> Residue type NAG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
rdpdb___459W> Residue type NDG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
In [7]:
#поправим идентификаторы
alignm[0].code = 'HYACE'
alignm[1].code = '1lmp'
In [8]:
#делаем выравнивание и сохраняем
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [9]:
! cat all_in_one.ali
>P1;HYACE sequence:: : : : :::-1.00:-1.00 MTKYVILLAVLAFALHCDAKRFTRCGLVQELRRLGFDETLMSNWVCLVENESGRFTDKIGKVNKNGSRDYGLFQI NDKYWCSKGTTPGKD--CNVTCNQLLTDDISVAATCAKKI-YKRHKFDAWYGWKNHCQHGLPDISDC-------* >P1;1lmp structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 KVYDRCELARALKASGMD----------------GYAGNSLPNWVCLSKWESSYNTQATNR-NTDGSTDYGIFQI NSRYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...*
В HYACE нет лиганда, далее добавим его вручную, но сначала посмотрим на результаты.
In [10]:
#построим модель
#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()
HYACE 1lmp
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
90 1 73 76 D C 8.895
END OF TABLE
read_to_681_> topology.submodel read from topology file: 3
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 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/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 11694 10727
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 : 139
Number of all, selected real atoms : 1112 1112
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10727 10727
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2394
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 : 886.4853
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 : 1136 0 1 0.008 0.008 18.369 1.000
2 Bond angle potential : 1532 1 6 2.003 2.003 125.60 1.000
3 Stereochemical cosine torsion poten: 734 0 29 47.203 47.203 252.35 1.000
4 Stereochemical improper torsion pot: 478 0 0 1.160 1.160 14.042 1.000
5 Soft-sphere overlap restraints : 2394 0 0 0.002 0.002 1.1112 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) : 2217 0 3 0.346 0.346 96.138 1.000
10 Distance restraints 2 (N-O) : 2375 0 5 0.373 0.373 127.63 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: 138 0 1 4.413 4.413 31.689 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 0 70.903 70.903 26.603 1.000
15 Sidechain Chi_2 dihedral restraints: 89 0 0 78.069 78.069 31.874 1.000
16 Sidechain Chi_3 dihedral restraints: 32 0 1 91.718 91.718 24.469 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 93.120 93.120 13.132 1.000
18 Disulfide distance restraints : 3 0 0 0.024 0.024 0.28661 1.000
19 Disulfide angle restraints : 6 0 0 2.272 2.272 0.68410 1.000
20 Disulfide dihedral angle restraints: 3 0 0 34.068 34.068 2.8123 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) : 1240 0 0 0.415 0.415 24.386 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: 137 22 17 29.885 68.472 72.926 1.000
26 Distance restraints 4 (SDCH-SDCH) : 466 0 0 0.586 0.586 22.383 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: HYACE.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: 15387.2246
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 2119 90D 90D N CA 713 714 124.72 107.00 17.72 5.10 107.00 17.72 5.10
-------------------------------------------------------------------------------------------------
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 3910 18D 19A C N 139 141 -121.27 -134.00 13.01 0.34 -62.50 -175.58 33.36
1 19A 19A N CA 141 142 144.29 147.00 -40.90
2 3911 19A 20K C N 144 146 -67.45 -70.20 5.91 0.48 -62.90 173.62 22.80
2 20K 20K N CA 146 147 145.63 140.40 -40.80
3 3912 20K 21R C N 153 155 -83.73 -72.10 30.87 2.60 -63.00 155.78 19.73
3 21R 21R N CA 155 156 113.30 141.90 -41.10
4 3913 21R 22F C N 164 166 -133.18 -124.20 9.01 0.33 -63.20 -174.64 30.32
4 22F 22F N CA 166 167 144.06 143.30 -44.30
5 3914 22F 23T C N 175 177 -83.49 -78.10 34.81 1.32 -63.20 135.24 18.70
5 23T 23T N CA 177 178 -175.81 149.80 -42.10
6 3915 23T 24R C N 182 184 -59.34 -72.10 30.54 2.08 -63.00 155.29 21.22
6 24R 24R N CA 184 185 114.15 141.90 -41.10
7 3917 25C 26G C N 199 201 73.48 78.70 9.94 0.15 82.20 166.38 8.52
7 26G 26G N CA 201 202 -157.64 -166.10 8.50
8 3918 26G 27L C N 203 205 -75.69 -70.70 24.71 1.69 -63.50 153.48 22.03
8 27L 27L N CA 205 206 165.80 141.60 -41.20
9 3919 27L 28V C N 211 213 -59.99 -62.40 3.50 0.40 -125.40 -176.21 10.34
9 28V 28V N CA 213 214 -44.94 -42.40 143.30
10 3920 28V 29Q C N 218 220 -72.20 -73.00 6.47 0.41 -63.80 174.79 25.27
10 29Q 29Q N CA 220 221 134.28 140.70 -40.30
11 3921 29Q 30E C N 227 229 -81.87 -69.30 21.67 1.24 -63.60 160.59 22.43
11 30E 30E N CA 229 230 160.15 142.50 -40.30
12 3922 30E 31L C N 236 238 -83.31 -108.50 44.42 2.08 -63.50 138.54 18.19
12 31L 31L N CA 238 239 95.91 132.50 -41.20
13 3924 32R 33R C N 255 257 -56.96 -72.10 16.90 1.14 -63.00 175.59 24.13
13 33R 33R N CA 257 258 134.39 141.90 -41.10
14 3925 33R 34L C N 266 268 -123.03 -108.50 14.56 0.70 -63.50 -177.24 22.75
14 34L 34L N CA 268 269 131.59 132.50 -41.20
15 3926 34L 35G C N 274 276 100.53 78.70 49.45 0.73 82.20 142.21 7.81
15 35G 35G N CA 276 277 149.53 -166.10 8.50
16 3929 37D 38E C N 297 299 57.97 54.60 5.39 0.30 -63.60 144.71 24.90
16 38E 38E N CA 299 300 38.20 42.40 -40.30
17 3943 51E 52S C N 411 413 -136.57 -64.10 79.73 8.46 -64.10 79.73 8.46
17 52S 52S N CA 413 414 -1.77 -35.00 -35.00
18 3952 60G 61K C N 479 481 -95.86 -118.00 89.76 4.01 -70.20 91.93 7.22
18 61K 61K N CA 481 482 52.12 139.10 140.40
19 3953 61K 62V C N 488 490 -65.03 -62.40 6.51 0.72 -125.40 -170.39 7.69
19 62V 62V N CA 490 491 -36.45 -42.40 143.30
20 3981 89K 90D C N 711 713 -132.67 -63.30 77.29 13.19 -63.30 77.29 13.19
20 90D 90D N CA 713 714 -74.08 -40.00 -40.00
21 4005 113I 114Y C N 884 886 -57.04 -98.40 42.24 1.93 -63.50 163.39 26.26
21 114Y 114Y N CA 886 887 119.86 128.40 -43.40
22 4029 137S 138D C N 1096 1098 -124.20 -63.30 80.86 9.39 -63.30 80.86 9.39
22 138D 138D N CA 1098 1099 13.19 -40.00 -40.00
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 3 13 67 91 117 113 137 138 176 186
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 139
Number of all, selected real atoms : 1112 1112
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10727 10727
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2293
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 887.4119
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 : 1136 0 1 0.007 0.007 17.422 1.000
2 Bond angle potential : 1532 1 6 1.951 1.951 118.15 1.000
3 Stereochemical cosine torsion poten: 734 0 25 46.799 46.799 247.57 1.000
4 Stereochemical improper torsion pot: 478 0 0 1.126 1.126 13.365 1.000
5 Soft-sphere overlap restraints : 2293 0 0 0.002 0.002 1.1559 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) : 2217 0 2 0.341 0.341 93.303 1.000
10 Distance restraints 2 (N-O) : 2375 0 6 0.385 0.385 133.64 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: 138 0 1 4.329 4.329 30.503 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 0 67.376 67.376 26.133 1.000
15 Sidechain Chi_2 dihedral restraints: 89 0 0 78.875 78.875 32.914 1.000
16 Sidechain Chi_3 dihedral restraints: 32 0 0 78.391 78.391 18.245 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 81.514 81.514 12.310 1.000
18 Disulfide distance restraints : 3 0 0 0.023 0.023 0.26857 1.000
19 Disulfide angle restraints : 6 0 0 2.300 2.300 0.70103 1.000
20 Disulfide dihedral angle restraints: 3 0 0 22.941 22.941 1.6275 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) : 1240 0 0 0.436 0.436 28.604 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: 137 19 21 31.266 60.674 86.371 1.000
26 Distance restraints 4 (SDCH-SDCH) : 466 0 0 0.585 0.585 25.126 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: HYACE.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: 14416.0605
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 2119 90D 90D N CA 713 714 123.57 107.00 16.57 4.77 107.00 16.57 4.77
-------------------------------------------------------------------------------------------------
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 3910 18D 19A C N 139 141 -82.62 -68.20 25.81 1.64 -62.50 153.72 26.23
1 19A 19A N CA 141 142 166.71 145.30 -40.90
2 3911 19A 20K C N 144 146 -85.94 -62.90 62.42 9.48 -62.90 62.42 9.48
2 20K 20K N CA 146 147 -98.82 -40.80 -40.80
3 3912 20K 21R C N 153 155 -60.72 -72.10 19.30 1.67 -63.00 161.43 21.65
3 21R 21R N CA 155 156 157.49 141.90 -41.10
4 3913 21R 22F C N 164 166 -63.76 -71.40 12.90 1.15 -63.20 164.60 22.89
4 22F 22F N CA 166 167 151.10 140.70 -44.30
5 3914 22F 23T C N 175 177 -66.50 -78.10 11.64 0.68 -63.20 169.09 21.90
5 23T 23T N CA 177 178 148.85 149.80 -42.10
6 3915 23T 24R C N 182 184 -124.61 -125.20 7.88 0.39 -63.00 -178.76 28.73
6 24R 24R N CA 184 185 148.46 140.60 -41.10
7 3918 26G 27L C N 203 205 -106.92 -108.50 62.51 3.36 -63.50 119.39 14.76
7 27L 27L N CA 205 206 70.01 132.50 -41.20
8 3919 27L 28V C N 211 213 -68.65 -62.40 7.89 0.96 -125.40 -172.11 10.44
8 28V 28V N CA 213 214 -37.59 -42.40 143.30
9 3921 29Q 30E C N 227 229 -92.58 -117.80 41.96 1.47 -63.60 146.46 18.09
9 30E 30E N CA 229 230 103.26 136.80 -40.30
10 3923 31L 32R C N 244 246 -160.71 -125.20 38.48 1.91 -63.00 -166.62 21.88
10 32R 32R N CA 246 247 125.78 140.60 -41.10
11 3925 33R 34L C N 266 268 -102.22 -70.70 59.27 3.67 -63.50 132.78 20.82
11 34L 34L N CA 268 269 -168.21 141.60 -41.20
12 3926 34L 35G C N 274 276 107.29 78.70 78.32 1.23 82.20 115.25 6.82
12 35G 35G N CA 276 277 120.99 -166.10 8.50
13 3929 37D 38E C N 297 299 60.69 54.60 8.96 0.53 -63.60 145.76 25.08
13 38E 38E N CA 299 300 35.83 42.40 -40.30
14 3943 51E 52S C N 411 413 -138.06 -64.10 82.31 8.59 -64.10 82.31 8.59
14 52S 52S N CA 413 414 1.13 -35.00 -35.00
15 3952 60G 61K C N 479 481 -103.78 -118.00 89.66 4.14 -70.20 95.89 7.66
15 61K 61K N CA 481 482 50.58 139.10 140.40
16 3953 61K 62V C N 488 490 -65.99 -62.40 8.26 0.91 -125.40 -172.10 7.63
16 62V 62V N CA 490 491 -34.96 -42.40 143.30
17 3981 89K 90D C N 711 713 -139.41 -63.30 83.96 14.32 -63.30 83.96 14.32
17 90D 90D N CA 713 714 -75.46 -40.00 -40.00
18 4005 113I 114Y C N 884 886 -53.77 -98.40 45.52 2.07 -63.50 163.10 26.38
18 114Y 114Y N CA 886 887 119.41 128.40 -43.40
19 4020 128H 129C C N 1030 1032 -116.53 -63.00 56.43 8.27 -63.00 56.43 8.27
19 129C 129C N CA 1032 1033 -23.23 -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 10 56 74 128 97 141 175 141 199
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
HYACE.B99990001.pdb 886.48529
HYACE.B99990002.pdb 887.41193
Получили 2 модели:
HYACE.B99990001.pdb 886.48529 HYACE.B99990002.pdb 887.41193
In [11]:
#получим список отстатков
#alignm[1].residues
#добавить в объект выравнивание последовательность из строки
#alignm.append_sequence()
In [12]:
from IPython.display import Image
Image(filename='mod1.1.png') #референс покрашен маджентой
Out[12]:
In [13]:
Image(filename='mod2.1.png')
Out[13]:
Добавим 3 остатка к последовательности, чтобы увидеть лиганд.
In [14]:
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()
HYACE 1lmp
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
90 1 73 76 D C 8.895
END OF TABLE
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/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 11694 10727
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.
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 : 139
Number of all, selected real atoms : 1112 1112
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10727 10727
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2327
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 : 878.9680
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 : 1136 0 1 0.007 0.007 18.160 1.000
2 Bond angle potential : 1532 1 7 2.056 2.056 129.96 1.000
3 Stereochemical cosine torsion poten: 734 0 24 46.706 46.706 248.80 1.000
4 Stereochemical improper torsion pot: 478 0 0 1.169 1.169 14.395 1.000
5 Soft-sphere overlap restraints : 2327 0 0 0.002 0.002 1.1918 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) : 2217 0 4 0.355 0.355 100.60 1.000
10 Distance restraints 2 (N-O) : 2375 0 6 0.409 0.409 143.25 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: 138 0 1 4.526 4.526 33.343 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 1 66.408 66.408 26.253 1.000
15 Sidechain Chi_2 dihedral restraints: 89 0 0 72.180 72.180 30.392 1.000
16 Sidechain Chi_3 dihedral restraints: 32 0 0 72.597 72.597 16.547 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 75.229 75.229 13.536 1.000
18 Disulfide distance restraints : 3 0 0 0.022 0.022 0.26088 1.000
19 Disulfide angle restraints : 6 0 0 2.236 2.236 0.66219 1.000
20 Disulfide dihedral angle restraints: 3 0 0 28.268 28.268 2.2967 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) : 1240 0 0 0.487 0.487 25.372 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: 137 18 15 28.054 64.990 53.533 1.000
26 Distance restraints 4 (SDCH-SDCH) : 466 0 0 0.586 0.586 20.412 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: HYACE.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: 14451.4336
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 2119 90D 90D N CA 713 714 123.34 107.00 16.34 4.70 107.00 16.34 4.70
-------------------------------------------------------------------------------------------------
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 3910 18D 19A C N 139 141 -63.12 -68.20 17.00 1.19 -62.50 169.98 27.83
1 19A 19A N CA 141 142 129.08 145.30 -40.90
2 3911 19A 20K C N 144 146 -123.21 -118.00 21.95 0.98 -62.90 169.85 25.66
2 20K 20K N CA 146 147 160.42 139.10 -40.80
3 3912 20K 21R C N 153 155 -66.59 -72.10 11.42 0.76 -63.00 173.03 23.14
3 21R 21R N CA 155 156 131.89 141.90 -41.10
4 3914 22F 23T C N 175 177 -98.97 -78.10 20.87 1.26 -63.20 171.81 24.42
4 23T 23T N CA 177 178 149.85 149.80 -42.10
5 3915 23T 24R C N 182 184 -106.04 -125.20 23.18 0.68 -63.00 174.07 20.96
5 24R 24R N CA 184 185 127.56 140.60 -41.10
6 3917 25C 26G C N 199 201 -121.60 -80.20 73.66 4.84 82.20 -171.98 14.69
6 26G 26G N CA 201 202 113.17 174.10 8.50
7 3918 26G 27L C N 203 205 -128.91 -108.50 31.60 1.45 -63.50 174.86 28.33
7 27L 27L N CA 205 206 156.63 132.50 -41.20
8 3919 27L 28V C N 211 213 -61.99 -62.40 2.74 0.32 -125.40 -177.07 10.27
8 28V 28V N CA 213 214 -45.10 -42.40 143.30
9 3920 28V 29Q C N 218 220 -69.70 -73.00 3.79 0.23 -63.80 179.24 26.05
9 29Q 29Q N CA 220 221 138.84 140.70 -40.30
10 3921 29Q 30E C N 227 229 -118.85 -117.80 9.22 0.44 -63.60 -177.69 27.43
10 30E 30E N CA 229 230 145.96 136.80 -40.30
11 3922 30E 31L C N 236 238 -108.96 -108.50 27.10 1.47 -63.50 153.49 19.24
11 31L 31L N CA 238 239 105.41 132.50 -41.20
12 3925 33R 34L C N 266 268 -56.67 -70.70 19.87 1.98 -63.50 163.27 22.29
12 34L 34L N CA 268 269 155.67 141.60 -41.20
13 3926 34L 35G C N 274 276 104.94 78.70 45.28 0.77 82.20 150.23 8.42
13 35G 35G N CA 276 277 157.00 -166.10 8.50
14 3929 37D 38E C N 297 299 53.32 54.60 1.27 0.15 -63.60 143.23 24.62
14 38E 38E N CA 299 300 42.42 42.40 -40.30
15 3943 51E 52S C N 411 413 -137.86 -64.10 82.37 8.56 -64.10 82.37 8.56
15 52S 52S N CA 413 414 1.66 -35.00 -35.00
16 3952 60G 61K C N 479 481 -69.02 -62.90 9.16 1.09 -70.20 174.38 12.61
16 61K 61K N CA 481 482 -33.98 -40.80 140.40
17 3981 89K 90D C N 711 713 -142.07 -63.30 88.17 15.05 -63.30 88.17 15.05
17 90D 90D N CA 713 714 -79.59 -40.00 -40.00
18 4005 113I 114Y C N 884 886 -55.52 -98.40 43.91 2.04 -63.50 162.53 26.20
18 114Y 114Y N CA 886 887 118.93 128.40 -43.40
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 6 7 73 74 120 119 123 168 159 166
<< 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 : 139
Number of all, selected real atoms : 1112 1112
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10727 10727
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2350
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 : 907.6264
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 : 1136 0 1 0.007 0.007 16.732 1.000
2 Bond angle potential : 1532 1 6 2.018 2.018 125.79 1.000
3 Stereochemical cosine torsion poten: 734 0 30 47.781 47.781 261.10 1.000
4 Stereochemical improper torsion pot: 478 0 0 1.176 1.176 14.755 1.000
5 Soft-sphere overlap restraints : 2350 0 0 0.003 0.003 1.8501 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) : 2217 0 2 0.350 0.350 97.765 1.000
10 Distance restraints 2 (N-O) : 2375 0 5 0.395 0.395 138.07 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: 138 0 1 4.539 4.539 33.524 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 0 75.115 75.115 34.657 1.000
15 Sidechain Chi_2 dihedral restraints: 89 0 0 68.219 68.219 34.086 1.000
16 Sidechain Chi_3 dihedral restraints: 32 0 0 81.562 81.562 22.302 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 89.237 89.237 12.117 1.000
18 Disulfide distance restraints : 3 0 0 0.020 0.020 0.21410 1.000
19 Disulfide angle restraints : 6 0 0 2.124 2.124 0.59788 1.000
20 Disulfide dihedral angle restraints: 3 0 0 29.409 29.409 2.5064 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) : 1240 0 0 0.471 0.471 19.614 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: 137 22 18 29.989 71.636 63.845 1.000
26 Distance restraints 4 (SDCH-SDCH) : 466 0 1 0.653 0.653 28.102 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: HYACE.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: 15807.1797
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 2119 90D 90D N CA 713 714 123.82 107.00 16.82 4.84 107.00 16.82 4.84
-------------------------------------------------------------------------------------------------
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 3910 18D 19A C N 139 141 -56.19 -68.20 20.40 1.29 -62.50 169.83 28.15
1 19A 19A N CA 141 142 128.82 145.30 -40.90
2 3911 19A 20K C N 144 146 -130.01 -118.00 40.55 2.08 -62.90 156.31 17.97
2 20K 20K N CA 146 147 100.37 139.10 -40.80
3 3912 20K 21R C N 153 155 -156.43 -125.20 53.40 1.77 -63.00 164.17 28.34
3 21R 21R N CA 155 156 -176.09 140.60 -41.10
4 3913 21R 22F C N 164 166 -89.22 -71.40 29.01 2.57 -63.20 164.18 21.11
4 22F 22F N CA 166 167 117.81 140.70 -44.30
5 3914 22F 23T C N 175 177 -86.11 -78.10 19.73 0.65 -63.20 151.81 21.00
5 23T 23T N CA 177 178 167.83 149.80 -42.10
6 3915 23T 24R C N 182 184 -70.89 -72.10 13.71 1.03 -63.00 169.53 22.38
6 24R 24R N CA 184 185 128.25 141.90 -41.10
7 3917 25C 26G C N 199 201 -118.16 -80.20 44.10 3.25 82.20 -145.58 16.59
7 26G 26G N CA 201 202 151.65 174.10 8.50
8 3919 27L 28V C N 211 213 -61.82 -62.40 0.77 0.09 -125.40 -174.95 10.38
8 28V 28V N CA 213 214 -42.91 -42.40 143.30
9 3920 28V 29Q C N 218 220 -67.35 -73.00 13.98 0.82 -63.80 168.25 24.55
9 29Q 29Q N CA 220 221 127.91 140.70 -40.30
10 3922 30E 31L C N 236 238 -62.25 -70.70 8.49 0.80 -63.50 176.36 24.42
10 31L 31L N CA 238 239 142.44 141.60 -41.20
11 3923 31L 32R C N 244 246 -141.77 -125.20 21.38 0.63 -63.00 -177.35 30.04
11 32R 32R N CA 246 247 154.11 140.60 -41.10
12 3924 32R 33R C N 255 257 -142.13 -125.20 25.28 0.79 -63.00 178.07 29.44
12 33R 33R N CA 257 258 159.37 140.60 -41.10
13 3925 33R 34L C N 266 268 -122.59 -108.50 29.14 1.40 -63.50 171.30 27.44
13 34L 34L N CA 268 269 158.02 132.50 -41.20
14 3926 34L 35G C N 274 276 86.00 78.70 29.57 0.56 82.20 156.79 7.80
14 35G 35G N CA 276 277 165.25 -166.10 8.50
15 3929 37D 38E C N 297 299 55.90 54.60 1.76 0.11 -63.60 144.66 24.88
15 38E 38E N CA 299 300 41.22 42.40 -40.30
16 3943 51E 52S C N 411 413 -136.84 -64.10 80.85 8.46 -64.10 80.85 8.46
16 52S 52S N CA 413 414 0.29 -35.00 -35.00
17 3952 60G 61K C N 479 481 -70.46 -62.90 15.21 1.75 -70.20 168.00 12.18
17 61K 61K N CA 481 482 -27.60 -40.80 140.40
18 3981 89K 90D C N 711 713 159.08 -96.50 105.32 4.29 -63.30 -163.30 22.13
18 90D 90D N CA 713 714 100.53 114.20 -40.00
19 4005 113I 114Y C N 884 886 -50.99 -98.40 48.38 2.20 -63.50 162.65 26.45
19 114Y 114Y N CA 886 887 118.76 128.40 -43.40
20 4007 115K 116R C N 905 907 -59.45 -125.20 66.37 2.44 -63.00 172.74 23.57
20 116R 116R N CA 907 908 131.61 140.60 -41.10
21 4008 116R 117H C N 916 918 51.96 -63.20 160.59 27.01 -63.20 160.59 27.01
21 117H 117H N CA 918 919 69.63 -42.30 -42.30
22 4009 117H 118K C N 926 928 -63.33 -62.90 21.05 2.76 -118.00 168.19 8.67
22 118K 118K N CA 928 929 -61.84 -40.80 139.10
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 9 76 71 127 92 142 166 167 195
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
HYACE.B99990001.pdb 878.96802
HYACE.B99990002.pdb 907.62640
Получичили чуть более хорошие структуры:
HYACE.B99990001.pdb 1034.49463 HYACE.B99990002.pdb 996.17755
In [15]:
Image(filename='mod1.2.png')
Out[15]:
In [16]:
Image(filename='mod2.2.png')
Out[16]:
Далее производим замену все аминокислот лизоцима на аланин.
In [17]:
alignm = modeller.alignment(env)
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
alanin = 'A' * 120 + '...'
alignm.append_sequence(alanin)
alignm[0].code = 'pdb'
alignm[1].code = 'alanin'
alignm.salign()
alignm.write(file='align_ala.ali', alignment_format='PIR')
! cat align_ala.ali
SALIGN_____> adding the next group to the alignment; iteration 1 >P1;pdb structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWCDDGRTPGAKNV CGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...* >P1;alanin sequence::1 : :+123 : :undefined:undefined:-1.00:-1.00 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA---------AAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA...*
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s = alignm[0]
pdb = alignm[1]
print(s.code, pdb.code)
#создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='align_ala.ali', knowns= pdb.code , sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
pdb alanin
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()
check_a_282E> Unable to read structural information for alignment
sequence: 1 alanin
This command requires structures.
--------------------------------------------------------------------------- ModellerError Traceback (most recent call last) <ipython-input-18-36f379918a98> in <module> 10 a.starting_model = 1 11 a.ending_model = 2 ---> 12 a.make() /anaconda2/lib/python3.6/site-packages/modeller/automodel/automodel.py in make(self, exit_stage) 131 132 self.outputs = [] --> 133 self.homcsr(exit_stage) 134 # Exit early? 135 if exit_stage >= 1: /anaconda2/lib/python3.6/site-packages/modeller/automodel/automodel.py in homcsr(self, exit_stage) 606 # modfile.delete(file='.tmp.ali') 607 --> 608 self.check_alignment(aln) 609 610 self._get_alignment_info(aln) /anaconda2/lib/python3.6/site-packages/modeller/automodel/automodel.py in check_alignment(self, aln) 559 def check_alignment(self, aln): 560 """Check the alignment for sanity""" --> 561 aln.check() 562 563 def _get_sequence_info(self, aln, tgt, known): /anaconda2/lib/python3.6/site-packages/modeller/alignment.py in check(self, io) 207 def check(self, io=None): 208 """Check alignment for modeling""" --> 209 self.check_structure_structure(io=io) 210 self.check_sequence_structure(io=io) 211 /anaconda2/lib/python3.6/site-packages/modeller/alignment.py in check_structure_structure(self, eqvdst, io) 216 io = self.env.io 217 f = _modeller.mod_alignment_check_structures --> 218 return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst) 219 220 def check_sequence_structure(self, gapdist=8.0, io=None): ModellerError: check_a_282E> Unable to read structural information for alignment sequence: 1 alanin This command requires structures.
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