Pr8: Гомологичное моделирование комплекса белка с лигандом
Я анализировала лизоцим Escherichia phage P2 (Bacteriophage P2) - LYS_BPP2. 1)Необходимо представить в отчёте результаты моделирования и результаты проверки качества структур. 2)Необходимо представить обсуждение результата
In [1]:
#загрузим все необходимое
import sys
import modeller
import _modeller
import modeller.automodel
import IPython
env=modeller.environ()
env.io.hetatm=True
alignm=modeller.alignment(env)
MODELLER 9.24, 2020/04/06, r11614
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2020 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, Windows Vista build 7601 Service Pack 1, SUNNYCAT-HP, SMP, unknown
Date and time of compilation : 2020/04/06 12:03:25
MODELLER executable type : x86_64-w64
Job starting time (YY/MM/DD HH:MM:SS): 2020/05/29 21:50:17
In [2]:
alignm.append(file='BPP2.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
alignm[0].code = 'BPP2'
alignm[1].code = '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 [3]:
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
all_in_one.ali¶
P1;BPP2 sequence:: : : : :::-1.00:-1.00 MPVINTHQNIAAFLDMLAVSEGTANHPLTKNRGYDVIVTGLDGKPEIFTDYSDHPFAHGRPAKVFNRRGEKSTAS GRYQQLYLFWPHYRKQLALPDFSPLSQDRLAIQLIRERGALDDIRAGRIERAISRCRNIWASLPGAGYGQREHSL EKLVTVWRTAGGVPA*
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 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYN----------------------TQATNRNTDGSTDY GIFQINSRYWCDDGRTPGAKNVCGIRCSQLLTDDLTV-----------AIRCAKRVVLDPNGIGAWVAWRLHCQN QDLRSYVAGCGV...*
In [4]:
## 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()
BPP2 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
----------------------------------------------
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.)
transfe_404W> At least one template is aligned with model residue 163:
but no coordinates could be transferred. This usually
occurs when your input files do not use the official
PDBv3 atom names. Please check your templates.
transfe_404W> At least one template is aligned with model residue 164:
but no coordinates could be transferred. This usually
occurs when your input files do not use the official
PDBv3 atom names. Please check your templates.
The following 1 residues contain 6-membered rings with poor geometries
after transfer from templates. Rebuilding rings from internal coordinates:
<Residue 34 (type TYR)>
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: 12539 11355
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 : 165
Number of all, selected real atoms : 1311 1311
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11355 11355
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3686
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 : 1854.1652
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 : 1344 0 2 0.008 0.008 26.933 1.000
2 Bond angle potential : 1822 1 13 2.542 2.542 220.63 1.000
3 Stereochemical cosine torsion poten: 880 0 40 49.033 49.033 311.53 1.000
4 Stereochemical improper torsion pot: 556 0 0 1.378 1.378 21.838 1.000
5 Soft-sphere overlap restraints : 3686 0 0 0.005 0.005 11.115 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) : 2406 1 15 0.566 0.566 209.28 1.000
10 Distance restraints 2 (N-O) : 2593 12 44 0.852 0.852 529.94 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: 164 0 5 5.322 5.322 54.005 1.000
14 Sidechain Chi_1 dihedral restraints: 135 0 2 81.700 81.700 57.210 1.000
15 Sidechain Chi_2 dihedral restraints: 109 0 1 77.187 77.187 54.922 1.000
16 Sidechain Chi_3 dihedral restraints: 48 0 1 77.550 77.550 35.269 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 91.938 91.938 15.155 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 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) : 938 0 0 0.618 0.618 41.187 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: 163 53 47 42.268 98.856 236.48 1.000
26 Distance restraints 4 (SDCH-SDCH) : 175 0 0 1.262 1.262 28.674 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: BPP2.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: 24842.6191
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 3150 164P 164P N CA 1299 1300 129.16 108.20 20.96 4.76 108.20 20.96 4.76
-------------------------------------------------------------------------------------------------
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 8623 68R 165A N O 523 1310 16.90 8.17 8.73 7.41 8.17 8.73 7.41
2 8631 69G 165A N O 534 1310 18.88 9.76 9.12 5.41 9.76 9.12 5.41
3 8640 70E 165A N O 538 1310 19.27 10.84 8.43 5.72 10.84 8.43 5.72
4 8669 72S 165A N O 556 1310 17.53 9.99 7.54 7.31 9.99 7.54 7.31
5 8693 73T 165A N O 562 1310 14.98 8.19 6.79 7.84 8.19 6.79 7.84
6 8719 74A 165A N O 569 1310 12.39 6.08 6.31 9.52 6.08 6.31 9.52
7 8944 81L 165A N O 625 1310 8.99 5.93 3.06 5.41 5.93 3.06 5.41
8 8975 82Y 165A N O 633 1310 12.48 8.00 4.48 6.51 8.00 4.48 6.51
9 9000 83L 165A N O 645 1310 14.48 9.46 5.02 5.45 9.46 5.02 5.45
10 9932 142G 165A N O 1127 1310 8.71 5.60 3.11 4.91 5.60 3.11 4.91
-------------------------------------------------------------------------------------------------
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 4605 3V 4I C N 21 23 -69.74 -63.40 16.85 3.00 -120.60 177.91 12.08
1 4I 4I N CA 23 24 -59.21 -43.60 130.30
2 4606 4I 5N C N 29 31 175.50 -63.20 127.36 20.63 -63.20 127.36 20.63
2 5N 5N N CA 31 32 -79.91 -41.10 -41.10
3 4616 14L 15D C N 108 110 -80.42 -63.30 61.15 6.70 -63.30 61.15 6.70
3 15D 15D N CA 110 111 18.70 -40.00 -40.00
4 4619 17L 18A C N 132 134 -53.80 -62.50 8.85 1.62 -134.00 -171.63 11.62
4 18A 18A N CA 134 135 -42.56 -40.90 147.00
5 4621 19V 20S C N 144 146 -54.62 -64.10 50.31 3.21 -72.40 124.46 7.94
5 20S 20S N CA 146 147 -84.41 -35.00 152.40
6 4622 20S 21E C N 150 152 -115.93 -117.80 65.83 3.27 -63.60 122.98 14.31
6 21E 21E N CA 152 153 70.99 136.80 -40.30
7 4634 32R 33G C N 243 245 -64.31 -62.40 6.53 1.08 82.20 156.83 12.01
7 33G 33G N CA 245 246 -47.44 -41.20 8.50
8 4637 35D 36V C N 267 269 -135.43 -125.40 18.00 0.58 -62.40 175.29 26.67
8 36V 36V N CA 269 270 158.24 143.30 -42.40
9 4641 39T 40G C N 296 298 -119.42 -80.20 41.62 2.23 82.20 -120.58 18.12
9 40G 40G N CA 298 299 -171.95 174.10 8.50
10 4642 40G 41L C N 300 302 -65.17 -70.70 25.99 1.77 -63.50 157.41 21.76
10 41L 41L N CA 302 303 116.20 141.60 -41.20
11 4643 41L 42D C N 308 310 -100.38 -70.90 68.66 2.31 -63.30 113.90 16.46
11 42D 42D N CA 310 311 -147.69 150.30 -40.00
12 4644 42D 43G C N 316 318 -68.40 -80.20 15.76 0.55 82.20 -143.77 6.66
12 43G 43G N CA 318 319 163.66 174.10 8.50
13 4645 43G 44K C N 320 322 -67.15 -70.20 7.51 0.47 -62.90 174.39 22.42
13 44K 44K N CA 322 323 133.54 140.40 -40.80
14 4647 45P 46E C N 336 338 -65.36 -69.30 10.19 0.64 -63.60 173.41 23.03
14 46E 46E N CA 338 339 133.10 142.50 -40.30
15 4648 46E 47I C N 345 347 -66.56 -63.40 4.60 0.86 -120.60 -174.69 8.61
15 47I 47I N CA 347 348 -46.95 -43.60 130.30
16 4649 47I 48F C N 353 355 -129.78 -124.20 20.72 0.82 -63.20 166.35 27.44
16 48F 48F N CA 355 356 163.26 143.30 -44.30
17 4650 48F 49T C N 364 366 -118.78 -124.80 12.23 0.69 -63.20 172.93 25.86
17 49T 49T N CA 366 367 154.15 143.50 -42.10
18 4651 49T 50D C N 371 373 -76.54 -70.90 19.16 0.70 -63.30 151.97 19.58
18 50D 50D N CA 373 374 168.61 150.30 -40.00
19 4652 50D 51Y C N 379 381 -61.24 -98.40 39.63 2.17 -63.50 158.03 25.19
19 51Y 51Y N CA 381 382 114.61 128.40 -43.40
20 4653 51Y 52S C N 391 393 -113.28 -136.60 24.94 0.79 -64.10 -175.97 11.40
20 52S 52S N CA 393 394 142.34 151.20 -35.00
21 4654 52S 53D C N 397 399 -83.82 -63.30 61.87 8.96 -63.30 61.87 8.96
21 53D 53D N CA 399 400 -98.36 -40.00 -40.00
22 4655 53D 54H C N 405 407 -62.84 -67.60 5.34 0.46 -63.20 175.26 21.89
22 54H 54H N CA 407 408 142.44 140.00 -42.30
23 4657 55P 56F C N 422 424 -114.29 -124.20 10.29 0.48 -63.20 177.16 28.01
23 56F 56F N CA 424 425 146.07 143.30 -44.30
24 4658 56F 57A C N 433 435 -162.79 -134.00 40.55 1.22 -62.50 175.12 33.99
24 57A 57A N CA 435 436 175.55 147.00 -40.90
25 4659 57A 58H C N 438 440 128.76 -125.60 105.68 3.63 -63.20 -116.71 40.66
25 58H 58H N CA 440 441 141.77 138.80 -42.30
26 4660 58H 59G C N 448 450 -68.61 -80.20 34.53 0.86 82.20 -158.88 6.76
26 59G 59G N CA 450 451 141.57 174.10 8.50
27 4661 59G 60R C N 452 454 -132.89 -63.00 97.21 17.45 -63.00 97.21 17.45
27 60R 60R N CA 454 455 -108.66 -41.10 -41.10
28 4664 62A 63K C N 475 477 -81.90 -118.00 91.34 3.81 -62.90 97.86 11.80
28 63K 63K N CA 477 478 55.19 139.10 -40.80
29 4680 78Y 79Q C N 605 607 62.91 55.10 13.99 1.64 -121.10 -163.33 9.24
29 79Q 79Q N CA 607 608 51.91 40.30 139.70
30 4686 84F 85W C N 662 664 -129.78 -63.00 73.23 10.39 -63.00 73.23 10.39
30 85W 85W N CA 664 665 -14.13 -44.20 -44.20
31 4689 87H 88Y C N 693 695 -120.37 -63.50 87.48 12.08 -63.50 87.48 12.08
31 88Y 88Y N CA 695 696 23.07 -43.40 -43.40
32 4691 89R 90K C N 716 718 -140.75 -62.90 89.40 12.12 -62.90 89.40 12.12
32 90K 90K N CA 718 719 3.15 -40.80 -40.80
33 4693 91Q 92L C N 734 736 -61.88 -63.50 20.21 2.72 -70.70 157.30 12.26
33 92L 92L N CA 736 737 -61.34 -41.20 141.60
34 4694 92L 93A C N 742 744 -91.51 -68.20 63.47 5.87 -62.50 130.43 20.16
34 93A 93A N CA 744 745 86.26 145.30 -40.90
35 4695 93A 94L C N 747 749 -70.62 -63.50 20.67 2.56 -70.70 163.40 12.37
35 94L 94L N CA 749 750 -21.80 -41.20 141.60
36 4696 94L 95P C N 755 757 -60.79 -64.50 38.05 2.65 -58.70 139.84 11.39
36 95P 95P N CA 757 758 109.33 147.20 -30.50
37 4697 95P 96D C N 762 764 -89.78 -96.50 10.25 0.43 54.50 158.48 14.13
37 96D 96D N CA 764 765 106.46 114.20 40.90
38 4699 97F 98S C N 781 783 -89.06 -72.40 48.56 3.42 -64.10 143.97 9.24
38 98S 98S N CA 783 784 106.79 152.40 -35.00
39 4700 98S 99P C N 787 789 -54.45 -58.70 29.44 2.78 -64.50 148.91 10.59
39 99P 99P N CA 789 790 -1.37 -30.50 147.20
40 4714 112E 113R C N 902 904 -45.85 -72.10 31.00 2.66 -63.00 161.43 20.70
40 113R 113R N CA 904 905 158.39 141.90 -41.10
41 4715 113R 114G C N 913 915 -127.91 -167.20 57.97 1.36 82.20 -165.80 15.09
41 114G 114G N CA 915 916 131.97 174.60 8.50
42 4716 114G 115A C N 917 919 -176.28 -134.00 47.63 1.09 -62.50 -171.59 36.85
42 115A 115A N CA 919 920 168.92 147.00 -40.90
43 4717 115A 116L C N 922 924 170.11 -108.50 84.35 3.80 -63.50 -152.83 36.39
43 116L 116L N CA 924 925 154.65 132.50 -41.20
44 4718 116L 117D C N 930 932 -142.48 -96.50 64.19 2.68 -63.30 179.42 27.25
44 117D 117D N CA 932 933 159.00 114.20 -40.00
45 4721 119I 120R C N 954 956 -167.99 -125.20 42.86 1.78 -63.00 -152.28 23.50
45 120R 120R N CA 956 957 138.14 140.60 -41.10
46 4722 120R 121A C N 965 967 -130.91 -134.00 7.28 0.45 -62.50 179.09 33.01
46 121A 121A N CA 967 968 153.59 147.00 -40.90
47 4724 122G 123R C N 974 976 97.83 -125.20 149.23 4.64 -63.00 -159.89 25.13
47 123R 123R N CA 976 977 -160.16 140.60 -41.10
48 4725 123R 124I C N 985 987 -109.24 -120.60 54.22 3.53 -63.40 140.75 24.76
48 124I 124I N CA 987 988 -176.68 130.30 -43.60
49 4738 136A 137S C N 1095 1097 -50.10 -72.40 23.08 1.79 -64.10 167.25 11.36
49 137S 137S N CA 1097 1098 158.34 152.40 -35.00
50 4739 137S 138L C N 1101 1103 91.00 -63.50 155.76 25.87 -63.50 155.76 25.87
50 138L 138L N CA 1103 1104 -60.95 -41.20 -41.20
51 4751 149S 150L C N 1190 1192 60.04 -70.70 151.59 15.28 -63.50 159.23 21.25
51 150L 150L N CA 1192 1193 -141.66 141.60 -41.20
52 4752 150L 151E C N 1198 1200 74.17 54.60 109.21 9.97 -69.30 143.66 11.14
52 151E 151E N CA 1200 1201 149.84 42.40 142.50
53 4758 156V 157W C N 1245 1247 -132.66 -124.90 79.16 4.01 -63.00 129.20 14.36
53 157W 157W N CA 1247 1248 64.62 143.40 -44.20
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 15 27 131 148 269 183 199 223 271 276
<< 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.
iupac_m_484W> Dihedral still outside +-90: -91.6331
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 : 165
Number of all, selected real atoms : 1311 1311
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11355 11355
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3871
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 : 2303.6675
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 : 1344 0 0 0.009 0.009 31.030 1.000
2 Bond angle potential : 1822 2 12 2.720 2.720 260.74 1.000
3 Stereochemical cosine torsion poten: 880 0 46 50.749 50.749 331.09 1.000
4 Stereochemical improper torsion pot: 556 0 1 1.708 1.708 31.107 1.000
5 Soft-sphere overlap restraints : 3871 0 1 0.006 0.006 17.635 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) : 2406 2 34 0.824 0.824 384.35 1.000
10 Distance restraints 2 (N-O) : 2593 16 73 1.010 1.010 701.81 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: 164 2 5 6.521 6.521 81.783 1.000
14 Sidechain Chi_1 dihedral restraints: 135 0 3 83.139 83.139 57.223 1.000
15 Sidechain Chi_2 dihedral restraints: 109 0 3 84.103 84.103 63.719 1.000
16 Sidechain Chi_3 dihedral restraints: 48 0 0 79.405 79.405 30.331 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 102.057 102.057 14.427 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 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) : 938 0 0 0.503 0.503 21.334 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: 163 55 43 42.842 100.224 249.80 1.000
26 Distance restraints 4 (SDCH-SDCH) : 175 0 0 1.330 1.330 27.294 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: BPP2.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: 27003.0449
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 9 : Distance restraints 1 (CA-CA)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 6419 62A 76G CA CA 473 581 6.12 4.40 1.72 4.61 4.40 1.72 4.61
-------------------------------------------------------------------------------------------------
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 8623 68R 165A N O 523 1310 16.55 8.17 8.38 7.11 8.17 8.38 7.11
2 8631 69G 165A N O 534 1310 18.94 9.76 9.17 5.45 9.76 9.17 5.45
3 8640 70E 165A N O 538 1310 19.48 10.84 8.64 5.87 10.84 8.64 5.87
4 8669 72S 165A N O 556 1310 17.70 9.99 7.72 7.49 9.99 7.72 7.49
5 8693 73T 165A N O 562 1310 14.93 8.19 6.75 7.79 8.19 6.75 7.79
6 8719 74A 165A N O 569 1310 12.31 6.08 6.23 9.40 6.08 6.23 9.40
7 8758 76G 64V N O 580 492 4.90 2.93 1.97 4.60 2.93 1.97 4.60
8 8944 81L 165A N O 625 1310 9.06 5.93 3.13 5.55 5.93 3.13 5.55
9 8975 82Y 165A N O 633 1310 12.52 8.00 4.52 6.56 8.00 4.52 6.56
10 9000 83L 165A N O 645 1310 14.49 9.46 5.03 5.46 9.46 5.03 5.46
11 9712 130R 127A N O 1034 1019 6.16 2.95 3.21 5.02 2.95 3.21 5.02
12 9732 131C 127A N O 1045 1019 6.58 2.93 3.65 7.90 2.93 3.65 7.90
13 9932 142G 165A N O 1127 1310 9.01 5.60 3.41 5.39 5.60 3.41 5.39
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4889 124I 124I CA C 988 993 -139.86 -180.00 40.14 8.02 -180.00 40.14 8.02
-------------------------------------------------------------------------------------------------
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 4604 2P 3V C N 14 16 -69.98 -62.40 13.65 2.18 -125.40 172.11 9.61
1 3V 3V N CA 16 17 -53.75 -42.40 143.30
2 4605 3V 4I C N 21 23 107.42 -120.60 132.24 8.91 -120.60 132.24 8.91
2 4I 4I N CA 23 24 138.59 130.30 130.30
3 4616 14L 15D C N 108 110 -80.02 -63.30 68.08 7.55 -63.30 68.08 7.55
3 15D 15D N CA 110 111 25.99 -40.00 -40.00
4 4621 19V 20S C N 144 146 -59.12 -64.10 48.36 3.24 -72.40 125.20 7.83
4 20S 20S N CA 146 147 -83.11 -35.00 152.40
5 4622 20S 21E C N 150 152 -100.94 -117.80 78.75 3.60 -63.60 106.91 12.62
5 21E 21E N CA 152 153 59.88 136.80 -40.30
6 4634 32R 33G C N 243 245 -63.24 -62.40 8.51 1.31 82.20 156.64 12.03
6 33G 33G N CA 245 246 -49.68 -41.20 8.50
7 4637 35D 36V C N 267 269 -148.30 -125.40 40.04 1.28 -62.40 165.50 26.15
7 36V 36V N CA 269 270 176.14 143.30 -42.40
8 4639 37I 38V C N 282 284 62.33 55.90 10.46 0.55 -125.40 -154.49 11.11
8 38V 38V N CA 284 285 31.25 39.50 143.30
9 4641 39T 40G C N 296 298 -66.29 -80.20 40.08 0.99 82.20 -163.95 6.69
9 40G 40G N CA 298 299 136.52 174.10 8.50
10 4642 40G 41L C N 300 302 -88.78 -70.70 20.80 1.49 -63.50 168.83 24.96
10 41L 41L N CA 302 303 151.87 141.60 -41.20
11 4643 41L 42D C N 308 310 -66.27 -70.90 13.46 0.89 -63.30 157.09 19.57
11 42D 42D N CA 310 311 162.94 150.30 -40.00
12 4644 42D 43G C N 316 318 -90.46 -80.20 52.67 1.58 82.20 -135.98 17.41
12 43G 43G N CA 318 319 -134.23 174.10 8.50
13 4645 43G 44K C N 320 322 -53.30 -70.20 16.93 1.21 -62.90 -179.90 22.88
13 44K 44K N CA 322 323 139.35 140.40 -40.80
14 4647 45P 46E C N 336 338 -131.64 -117.80 41.62 1.78 -63.60 158.94 25.00
14 46E 46E N CA 338 339 176.06 136.80 -40.30
15 4649 47I 48F C N 353 355 -100.16 -71.40 62.74 5.56 -63.20 134.42 16.38
15 48F 48F N CA 355 356 84.94 140.70 -44.30
16 4650 48F 49T C N 364 366 -117.53 -63.20 81.14 13.66 -63.20 81.14 13.66
16 49T 49T N CA 366 367 -102.37 -42.10 -42.10
17 4651 49T 50D C N 371 373 -55.93 -70.90 40.11 1.38 -63.30 153.26 19.37
17 50D 50D N CA 373 374 113.09 150.30 -40.00
18 4652 50D 51Y C N 379 381 -118.96 -98.40 33.75 2.86 -63.50 155.28 22.14
18 51Y 51Y N CA 381 382 101.63 128.40 -43.40
19 4653 51Y 52S C N 391 393 50.48 -72.40 127.80 9.95 -64.10 178.96 13.41
19 52S 52S N CA 393 394 -172.47 152.40 -35.00
20 4654 52S 53D C N 397 399 -96.65 -70.90 39.64 1.48 -63.30 143.51 19.85
20 53D 53D N CA 399 400 -179.57 150.30 -40.00
21 4655 53D 54H C N 405 407 56.76 56.30 100.40 8.92 -63.20 -146.59 22.82
21 54H 54H N CA 407 408 141.20 40.80 -42.30
22 4658 56F 57A C N 433 435 172.49 -134.00 64.33 1.57 -62.50 -174.98 36.74
22 57A 57A N CA 435 436 -177.30 147.00 -40.90
23 4659 57A 58H C N 438 440 -96.27 -125.60 34.12 0.87 -63.20 166.98 19.04
23 58H 58H N CA 440 441 121.37 138.80 -42.30
24 4660 58H 59G C N 448 450 145.66 -167.20 49.45 1.34 82.20 163.95 10.91
24 59G 59G N CA 450 451 159.68 174.60 8.50
25 4661 59G 60R C N 452 454 -92.01 -72.10 22.71 1.51 -63.00 168.60 24.77
25 60R 60R N CA 454 455 152.82 141.90 -41.10
26 4664 62A 63K C N 475 477 -84.27 -118.00 85.81 3.59 -62.90 103.24 12.40
26 63K 63K N CA 477 478 60.20 139.10 -40.80
27 4669 67R 68R C N 521 523 -74.44 -63.00 14.66 1.81 -125.20 179.85 7.44
27 68R 68R N CA 523 524 -31.94 -41.10 140.60
28 4670 68R 69G C N 532 534 92.05 82.20 37.18 1.32 -62.40 155.07 28.22
28 69G 69G N CA 534 535 -27.34 8.50 -41.20
29 4680 78Y 79Q C N 605 607 65.22 55.10 17.05 2.04 -121.10 -166.34 9.09
29 79Q 79Q N CA 607 608 54.02 40.30 139.70
30 4689 87H 88Y C N 693 695 -119.72 -63.50 88.61 12.23 -63.50 88.61 12.23
30 88Y 88Y N CA 695 696 25.09 -43.40 -43.40
31 4691 89R 90K C N 716 718 -141.00 -62.90 83.86 12.07 -62.90 83.86 12.07
31 90K 90K N CA 718 719 -10.25 -40.80 -40.80
32 4694 92L 93A C N 742 744 89.44 55.40 158.50 6.97 -62.50 169.75 28.68
32 93A 93A N CA 744 745 -116.60 38.20 -40.90
33 4695 93A 94L C N 747 749 79.02 -70.70 158.08 12.48 -70.70 158.08 12.48
33 94L 94L N CA 749 750 90.87 141.60 141.60
34 4696 94L 95P C N 755 757 -86.97 -64.50 25.96 1.98 -58.70 171.65 16.52
34 95P 95P N CA 757 758 160.20 147.20 -30.50
35 4697 95P 96D C N 762 764 -126.08 -96.50 54.74 2.26 54.50 -178.52 22.51
35 96D 96D N CA 764 765 68.14 114.20 40.90
36 4699 97F 98S C N 781 783 -70.50 -72.40 13.76 0.75 -64.10 173.89 12.23
36 98S 98S N CA 783 784 138.77 152.40 -35.00
37 4700 98S 99P C N 787 789 -76.54 -58.70 40.77 2.38 -64.50 141.56 11.21
37 99P 99P N CA 789 790 6.16 -30.50 147.20
38 4714 112E 113R C N 902 904 27.95 -72.10 115.94 9.92 -63.00 149.31 17.06
38 113R 113R N CA 904 905 -159.51 141.90 -41.10
39 4715 113R 114G C N 913 915 -139.99 -167.20 27.61 0.65 82.20 -140.56 16.42
39 114G 114G N CA 915 916 179.27 174.60 8.50
40 4716 114G 115A C N 917 919 -140.20 -134.00 39.91 2.11 -62.50 153.75 29.34
40 115A 115A N CA 919 920 -173.57 147.00 -40.90
41 4717 115A 116L C N 922 924 -129.51 -108.50 22.38 1.17 -63.50 178.62 22.06
41 116L 116L N CA 924 925 124.78 132.50 -41.20
42 4719 117D 118D C N 938 940 -65.40 -70.90 19.28 1.23 -63.30 151.24 18.80
42 118D 118D N CA 940 941 168.78 150.30 -40.00
43 4721 119I 120R C N 954 956 -151.24 -125.20 26.89 0.91 -63.00 -167.06 32.05
43 120R 120R N CA 956 957 147.32 140.60 -41.10
44 4722 120R 121A C N 965 967 -53.41 -68.20 29.42 1.90 -62.50 161.02 26.84
44 121A 121A N CA 967 968 119.86 145.30 -40.90
45 4723 121A 122G C N 970 972 56.75 78.70 23.25 0.94 82.20 168.87 9.46
45 122G 122G N CA 972 973 -158.44 -166.10 8.50
46 4724 122G 123R C N 974 976 157.97 -125.20 77.38 2.87 -63.00 -141.08 38.52
46 123R 123R N CA 976 977 149.79 140.60 -41.10
47 4725 123R 124I C N 985 987 -60.24 -120.60 60.36 4.17 -63.40 173.36 28.52
47 124I 124I N CA 987 988 129.73 130.30 -43.60
48 4727 125E 126R C N 1002 1004 -155.83 -125.20 113.11 4.71 -63.00 115.92 21.07
48 126R 126R N CA 1004 1005 -110.52 140.60 -41.10
49 4729 127A 128I C N 1018 1020 -154.81 -63.40 93.81 17.34 -63.40 93.81 17.34
49 128I 128I N CA 1020 1021 -64.66 -43.60 -43.60
50 4738 136A 137S C N 1095 1097 70.97 -72.40 158.73 12.68 -64.10 170.76 15.37
50 137S 137S N CA 1097 1098 -139.48 152.40 -35.00
51 4740 138L 139P C N 1109 1111 -66.73 -64.50 5.06 0.29 -58.70 177.95 15.36
51 139P 139P N CA 1111 1112 151.74 147.20 -30.50
52 4741 139P 140G C N 1116 1118 119.58 82.20 55.54 1.66 -62.40 178.23 31.48
52 140G 140G N CA 1118 1119 -32.58 8.50 -41.20
53 4751 149S 150L C N 1190 1192 55.25 60.20 11.58 0.40 -63.50 143.89 26.46
53 150L 150L N CA 1192 1193 40.06 29.60 -41.20
54 4759 157W 158R C N 1259 1261 46.99 57.30 18.74 0.99 -72.10 148.23 9.67
54 158R 158R N CA 1261 1262 53.65 38.00 141.90
55 4760 158R 159T C N 1270 1272 54.45 55.90 17.06 1.30 -124.80 -143.74 7.85
55 159T 159T N CA 1272 1273 22.51 39.50 143.50
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 35 40 179 181 210 193 224 291 264 274
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
BPP2.B99990001.pdb 1854.16516
BPP2.B99990002.pdb 2303.66748
In [6]:
cmd.reinitialize()
cmd.load('BPP2.B99990001.pdb')
cmd.load('HYACE.B99990002.pdb')
cmd.do('''
fetch 1lmp, async=0
remove solvent
bg_color white
color spectrum rainbow, 1lmp
''')
In [7]:
Видно что структуры накладываются плохо. Лизоцим BPP2 имеет больше аминокислот в составе,
то, что не выровнялось, программа построила как длинную петлю. BPP2 зеленый, 1lmp розовый
Out[7]:
In [ ]:
Создание лиганда
In [8]:
seq_lig = ''
for res in alignm[0].residues:
seq_lig += res.code
for lig in alignm[1].residues[-3:]:
seq_lig += lig.code
alignm.append_sequence(seq_lig)
alignm[2].code = 'BPP2_lig'
del alignm[0]
alignm.salign()
alignm.write(file='all_in_two.ali', alignment_format='PIR')
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 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYN----------------------TQATNRNTDGSTDY GIFQINSRYWCDDGRTPGAKNVCGIRCSQLL--------------TDDLTVAIRCAKRVVLDPNGIGAWVAWRLH CQNQDLRSYVAGCGV...*
P1;BPP2_lig sequence::1 : :+168 : :undefined:undefined:-1.00:-1.00 MPVINTHQNIAAFLDMLAVSEGTANHPLTKNRGYDVIVTGLDGKPEIFTDYSDHPFAHGRPAKVFNRRGEKSTAS GRYQQLYLFWPHYRKQLALPDFSPLSQDRLAIQLIRERGALDDIRAGRIERAISRCRNIWASLPGAGYGQREHSL EKLVTVWRTAGGVPA...*
In [10]:
## Выбираем объект для моделирования
s = alignm[1]
pdb = alignm[0]
print(s.code, pdb.code)
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='all_in_two.ali', knowns= pdb.code, sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
In [12]:
Добавление лиганда улучшило качество выравнивания, но также есть длинные петли и лиганды плохо накладываются друг на друга
Out[12]:
In [ ]:
Перемещение лиганда
In [19]:
class mymodel(modeller.automodel.automodel):
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
for x,y in [ ('OG:131', 'C3:168'), ('OG:130','CA:105')]:
rsr.add(modeller.forms.gaussian(group=modeller.physical.xy_distance,
feature=modeller.features.distance(at[x],at[y]),
mean=3.0, stdev=0.1))
from modeller import *
from modeller.automodel import *
a = mymodel(env, alnfile='all_in_two.ali', knowns=pdb.code, sequence=s.code)
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
In [22]:
Выравнивание лигандов не повлияло на качество выравнивания
Out[22]:
In [ ]:
Вручную создали файл fasta с последовательностью аланинов(столько же как и в белке)
In [25]:
alignm=modeller.alignment(env)
alignm.append(file='BP22_a.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 = 'ala'
alignm[1].code = '1lmp'
alignm.salign()
alignm.write(file='all_in_three.ali', alignment_format='PIR')
In [27]:
with open("all_in_one_3.ali", 'r') as align:
seq = align.read().split("*")
seq[0] = seq[0][:-2] + "..."
seq[1] = seq[1][:-3] + "-..."
new = "*".join(seq)
with open("all_in_3_lig.ali", 'w') as out:
out.write(new)
In [ ]:
>P1;ala
sequence:: : : : :::-1.00:-1.00
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA...*
>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
KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRY-------WCDDGR
TPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV-...*
In [31]:
## 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_three.ali', knowns= pdb.code , sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
In [33]:
Полиаланиновый лизин сполучился совсем другой структуры и не выравнялся с 1lmp
Out[33]:
