HW 6. Didkovskaya Natalia¶
Гомологичное моделирование комплекса белка с лигандом¶
In [1]:
import sys
import modeller
import _modeller
import modeller.automodel
In [2]:
import nglview
import ipywidgets
from IPython.display import Image
Буду использовать лизоцим курочки. P00698. Gallus gallus
Часть 1¶
Объект выравнивания (alignm):
In [3]:
env=modeller.environ()
env.io.hetatm=True
alignm=modeller.alignment(env)
MODELLER 9.19, 2017/07/19, r11078
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2017 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux shadbox 3.2.0-29-generic x86_64
Date and time of compilation : 2017/07/19 14:40:43
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2017/12/10 13:36:26
Добавим в объект выравнивания информацию о выбранном белкке:
In [4]:
alignm.append(file='P00698.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.
Я не очень понимаю, зачем нужно править идентификатор.. Пока что кажется, что все правильно
In [5]:
alignm
Out[5]:
Alignment of Sequence 'sp|P00698|LYSC_CHICK', Structure '1lmp'
Поэтому перехожу к следующему шагу. Делаем выравнивание и сохранем
In [6]:
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
В содержимом файла all_in_one.ali появилась аминокислотная последовательность куриного лизомицина и белка-заготовки, ничего страшного в глаза пока не бросается
Памятка:
The first line loads in the automodel class and prepares it for use. We then create an automodel object, call it 'a', and set parameters to guide the model building procedure. alnfile names the file that contains the target-template alignment in the PIR format. knowns defines the known template structure(s) in alnfile ("TvLDH-1bdmA.ali"). sequence defines the name of the target sequence in alnfile. assess_methods requests one or more assessment scores (discussed in more detail in the next section). starting_model and ending_model define the number of models that are calculated (their indices will run from 1 to 5). The last line in the file calls the make method that actually calculates the models.
Построим модель:
In [7]:
## Выбираем объект для моделирования
s = alignm[0]
pdb = alignm[1]
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='all_in_one.ali', knowns= pdb.code , sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
read_to_681_> topology.submodel read from topology file: 3
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 4
The following 1 residues contain 6-membered rings with poor geometries
after transfer from templates. Rebuilding rings from internal coordinates:
<Residue 52 (type PHE)>
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: 12801 11802
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 147
Number of all, selected real atoms : 1135 1135
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11802 11802
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2392
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 : 758.1279
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 : 1157 0 0 0.006 0.006 11.178 1.000
2 Bond angle potential : 1566 0 4 2.055 2.055 133.89 1.000
3 Stereochemical cosine torsion poten: 738 0 27 48.906 48.906 272.75 1.000
4 Stereochemical improper torsion pot: 468 0 0 1.349 1.349 19.379 1.000
5 Soft-sphere overlap restraints : 2392 0 0 0.001 0.001 0.40765 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2404 0 0 0.106 0.106 31.526 1.000
10 Distance restraints 2 (N-O) : 2562 0 0 0.146 0.146 64.685 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: 146 0 2 4.280 4.280 31.540 1.000
14 Sidechain Chi_1 dihedral restraints: 120 0 0 70.984 70.984 18.141 1.000
15 Sidechain Chi_2 dihedral restraints: 86 0 0 79.560 79.560 43.141 1.000
16 Sidechain Chi_3 dihedral restraints: 29 0 0 85.395 85.395 21.413 1.000
17 Sidechain Chi_4 dihedral restraints: 18 0 0 92.041 92.041 12.366 1.000
18 Disulfide distance restraints : 4 0 0 0.008 0.008 0.39303E-01 1.000
19 Disulfide angle restraints : 8 0 0 1.786 1.786 0.56371 1.000
20 Disulfide dihedral angle restraints: 4 0 0 28.199 28.199 3.1127 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) : 1609 0 0 0.342 0.342 35.233 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: 145 16 11 24.118 58.325 22.832 1.000
26 Distance restraints 4 (SDCH-SDCH) : 738 0 0 0.572 0.572 35.929 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: sp|P00698|LYSC_CHICK.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: 14786.3799
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 3946 1M 2R C N 7 9 -84.53 -72.10 19.29 1.25 -63.00 163.67 23.59
1 2R 2R N CA 9 10 156.66 141.90 -41.10
2 3947 2R 3S C N 18 20 -80.81 -72.40 27.91 1.38 -64.10 146.93 11.72
2 3S 3S N CA 20 21 179.02 152.40 -35.00
3 3948 3S 4L C N 24 26 -84.60 -108.50 29.44 1.30 -63.50 157.94 20.81
3 4L 4L N CA 26 27 115.32 132.50 -41.20
4 3949 4L 5L C N 32 34 -83.67 -70.70 24.41 1.51 -63.50 157.82 23.12
4 5L 5L N CA 34 35 162.28 141.60 -41.20
5 3950 5L 6I C N 40 42 74.01 -120.60 165.39 11.54 -120.60 165.39 11.54
5 6I 6I N CA 42 43 128.51 130.30 130.30
6 3951 6I 7L C N 48 50 -119.98 -108.50 12.12 0.63 -63.50 178.95 22.33
6 7L 7L N CA 50 51 128.61 132.50 -41.20
7 3953 8V 9L C N 63 65 -93.07 -108.50 23.57 1.08 -63.50 158.67 20.53
7 9L 9L N CA 65 66 114.69 132.50 -41.20
8 3955 10C 11F C N 77 79 -75.26 -71.40 15.65 1.35 -63.20 170.26 22.84
8 11F 11F N CA 79 80 125.53 140.70 -44.30
9 3956 11F 12L C N 88 90 -122.58 -108.50 17.17 0.94 -63.50 174.20 21.63
9 12L 12L N CA 90 91 122.68 132.50 -41.20
10 3958 13P 14L C N 103 105 -82.71 -108.50 47.79 2.25 -63.50 134.85 17.71
10 14L 14L N CA 105 106 92.27 132.50 -41.20
11 3959 14L 15A C N 111 113 -147.79 -134.00 14.64 0.68 -62.50 -163.50 36.77
11 15A 15A N CA 113 114 142.08 147.00 -40.90
12 3960 15A 16A C N 116 118 161.70 -134.00 65.38 1.75 -62.50 -149.92 41.47
12 16A 16A N CA 118 119 158.82 147.00 -40.90
13 3961 16A 17L C N 121 123 -105.80 -108.50 36.32 1.93 -63.50 143.85 18.04
13 17L 17L N CA 123 124 96.29 132.50 -41.20
14 3962 17L 18G C N 129 131 -79.63 -80.20 18.87 0.71 82.20 -141.55 7.23
14 18G 18G N CA 131 132 155.24 174.10 8.50
15 3963 18G 19K C N 133 135 -115.88 -118.00 8.60 0.38 -62.90 179.56 21.05
15 19K 19K N CA 135 136 130.76 139.10 -40.80
16 3998 53E 54S C N 410 412 -134.73 -64.10 78.92 8.20 -64.10 78.92 8.20
16 54S 54S N CA 412 413 0.21 -35.00 -35.00
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 6 6 40 80 109 108 147 158 194 181
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 147
Number of all, selected real atoms : 1135 1135
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11802 11802
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2301
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 : 786.1551
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 : 1157 0 0 0.006 0.006 11.178 1.000
2 Bond angle potential : 1566 0 6 2.089 2.089 138.84 1.000
3 Stereochemical cosine torsion poten: 738 0 25 48.035 48.035 261.52 1.000
4 Stereochemical improper torsion pot: 468 0 0 1.248 1.248 17.339 1.000
5 Soft-sphere overlap restraints : 2301 0 0 0.001 0.001 0.38577 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2404 0 0 0.112 0.112 34.043 1.000
10 Distance restraints 2 (N-O) : 2562 0 3 0.172 0.172 85.590 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: 146 0 4 4.719 4.719 38.346 1.000
14 Sidechain Chi_1 dihedral restraints: 120 0 0 61.415 61.415 13.474 1.000
15 Sidechain Chi_2 dihedral restraints: 86 0 2 68.296 68.296 37.700 1.000
16 Sidechain Chi_3 dihedral restraints: 29 0 0 88.651 88.651 19.520 1.000
17 Sidechain Chi_4 dihedral restraints: 18 0 0 97.736 97.736 15.365 1.000
18 Disulfide distance restraints : 4 0 0 0.007 0.007 0.32413E-01 1.000
19 Disulfide angle restraints : 8 0 0 1.680 1.680 0.49848 1.000
20 Disulfide dihedral angle restraints: 4 0 0 30.289 30.289 3.5339 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) : 1609 0 0 0.359 0.359 33.151 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: 145 17 15 20.117 58.823 23.910 1.000
26 Distance restraints 4 (SDCH-SDCH) : 738 0 2 0.683 0.683 51.728 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: sp|P00698|LYSC_CHICK.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: 14693.8379
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 3946 1M 2R C N 7 9 54.25 57.30 15.02 0.80 -63.00 150.15 27.23
1 2R 2R N CA 9 10 52.70 38.00 -41.10
2 3947 2R 3S C N 18 20 -76.17 -72.40 15.63 0.80 -64.10 157.89 12.20
2 3S 3S N CA 20 21 167.57 152.40 -35.00
3 3948 3S 4L C N 24 26 -109.66 -108.50 47.93 2.58 -63.50 145.88 23.11
3 4L 4L N CA 26 27 -179.58 132.50 -41.20
4 3949 4L 5L C N 32 34 -63.06 -70.70 8.20 0.82 -63.50 174.21 24.16
4 5L 5L N CA 34 35 144.59 141.60 -41.20
5 3951 6I 7L C N 48 50 -81.16 -70.70 12.07 0.86 -63.50 172.09 24.94
5 7L 7L N CA 50 51 147.62 141.60 -41.20
6 3953 8V 9L C N 63 65 -107.13 -108.50 9.10 0.50 -63.50 -177.41 28.03
6 9L 9L N CA 65 66 141.49 132.50 -41.20
7 3955 10C 11F C N 77 79 -103.94 -124.20 65.28 3.48 -63.20 117.62 19.02
7 11F 11F N CA 79 80 -154.64 143.30 -44.30
8 3956 11F 12L C N 88 90 -45.62 -70.70 33.54 2.19 -63.50 161.52 23.49
8 12L 12L N CA 90 91 119.32 141.60 -41.20
9 3958 13P 14L C N 103 105 -73.43 -70.70 29.11 2.10 -63.50 148.55 21.21
9 14L 14L N CA 105 106 170.58 141.60 -41.20
10 3959 14L 15A C N 111 113 -56.34 -68.20 13.75 0.92 -62.50 179.35 29.70
10 15A 15A N CA 113 114 138.35 145.30 -40.90
11 3960 15A 16A C N 116 118 -138.77 -134.00 30.10 1.59 -62.50 161.52 30.55
11 16A 16A N CA 118 119 176.72 147.00 -40.90
12 3961 16A 17L C N 121 123 -59.82 -70.70 16.78 1.05 -63.50 170.07 23.83
12 17L 17L N CA 123 124 128.83 141.60 -41.20
13 3962 17L 18G C N 129 131 157.54 -167.20 47.35 1.73 82.20 154.15 10.86
13 18G 18G N CA 131 132 142.99 174.60 8.50
14 3963 18G 19K C N 133 135 -117.88 -118.00 5.29 0.26 -62.90 -176.93 21.43
14 19K 19K N CA 135 136 133.82 139.10 -40.80
15 3998 53E 54S C N 410 412 -139.34 -64.10 87.16 8.65 -64.10 87.16 8.65
15 54S 54S N CA 412 413 9.01 -35.00 -35.00
16 4078 133C 134K C N 1022 1024 -51.32 -62.90 28.04 3.23 -70.20 154.42 11.62
16 134K 134K N CA 1024 1025 -66.34 -40.80 140.40
17 4079 134K 135G C N 1031 1033 -75.37 -62.40 16.61 2.41 82.20 162.40 12.08
17 135G 135G N CA 1033 1034 -30.82 -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 2 6 54 67 111 94 132 168 170 175
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
sp|P00698|LYSC_CHICK.B99990001.pdb 758.12793
sp|P00698|LYSC_CHICK.B99990002.pdb 786.15509
Памятка по результатам:
The most important output file is "model-single.log", which reports warnings, errors and other useful information including the input restraints used for modeling that remain violated in the final model.
As you can see, the log file gives a summary of all the models built. For each model, it lists the file name, which contains the coordinates of the model in PDB format. The models can be viewed by any program that reads the PDB format, such as Chimera. The log also shows the score(s) of each model, which are further discussed below. (Note that the actual numbers may be slightly different on your machine - this is nothing to worry about.)
Посмотрим на результат:
In [8]:
#nglview.show_structure_file('sp|P00698|LYSC_CHICK.B99990001.pdb')
Image(filename = "/Users/Nataliyadi/Downloads/6hw/1.png", width=500, height=500)
Out[8]:
In [7]:
#nglview.show_structure_file('sp|P00698|LYSC_CHICK.B99990002.pdb')
Image(filename = "/Users/Nataliyadi/Downloads/6hw/2.png", width=500, height=500)
Out[7]:
In [6]:
## И заодно посмотрим на исходный белок
#nglview.show_structure_file('1lmp.pdb')
Image(filename = "/Users/Nataliyadi/Downloads/6hw/3.png", width=500, height=500)
Out[6]:
Часть 2¶
Необходимо к лизоциму курочки добавить лиганд. Это можно сделать, дописав в конце последовательности три точки.
In [12]:
# Получить список остаков 1lmp
alignm[1].residues[129:]
Out[12]:
[Residue 130:A (type NAG), Residue 131:A (type NAG), Residue 132:A (type NDG)]
In [13]:
# Добавим три точки к курочке
dots = '' #новая строчка, эквивалентная последовательности из alignm[0].residues, но с тремя точками на коцне
for r in alignm[0].residues:
dots += r.code
dots += '...'
In [14]:
dots
Out[14]:
'MRSLLILVLCFLPLAALGKVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL...'
In [15]:
alignm.append_sequence(dots)
In [17]:
## Выбираем объект для моделирования
s = alignm[2]
pdb = alignm[1]
s.code = 'plus_ligand'
In [18]:
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 [19]:
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()
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 10 147
atom names : C +N
atom indices : 1133 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 10 147
atom names : C CA +N O
atom indices : 1133 1128 0 1134
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
The following 1 residues contain 6-membered rings with poor geometries
after transfer from templates. Rebuilding rings from internal coordinates:
<Residue 52 (type PHE)>
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 14202 13203
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 : 150
Number of all, selected real atoms : 1178 1178
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13203 13203
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2519
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 : 888.7398
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 : 1157 0 0 0.006 0.006 11.805 1.000
2 Bond angle potential : 1566 0 6 2.153 2.153 145.54 1.000
3 Stereochemical cosine torsion poten: 738 0 28 48.447 48.447 270.87 1.000
4 Stereochemical improper torsion pot: 468 0 0 1.418 1.418 21.445 1.000
5 Soft-sphere overlap restraints : 2519 2 2 0.008 0.008 17.013 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2404 0 0 0.103 0.103 31.707 1.000
10 Distance restraints 2 (N-O) : 2562 0 0 0.146 0.146 69.060 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: 146 0 2 4.324 4.324 32.187 1.000
14 Sidechain Chi_1 dihedral restraints: 120 0 1 79.005 79.005 33.343 1.000
15 Sidechain Chi_2 dihedral restraints: 86 0 0 78.208 78.208 42.666 1.000
16 Sidechain Chi_3 dihedral restraints: 29 0 0 73.899 73.899 15.662 1.000
17 Sidechain Chi_4 dihedral restraints: 18 0 0 83.625 83.625 11.175 1.000
18 Disulfide distance restraints : 4 0 0 0.006 0.006 0.28444E-01 1.000
19 Disulfide angle restraints : 8 0 0 2.713 2.713 1.3006 1.000
20 Disulfide dihedral angle restraints: 4 0 0 32.350 32.350 3.4326 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) : 1609 0 0 0.505 0.505 77.781 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: 145 14 9 22.377 57.187 19.577 1.000
26 Distance restraints 4 (SDCH-SDCH) : 738 0 2 0.814 0.814 72.825 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.028 0.028 11.317 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: plus_ligand.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 15935.2754
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 3946 1M 2R C N 7 9 -70.81 -72.10 6.49 0.53 -63.00 170.83 23.60
1 2R 2R N CA 9 10 148.25 141.90 -41.10
2 3947 2R 3S C N 18 20 -85.51 -72.40 34.37 1.64 -64.10 142.44 11.73
2 3S 3S N CA 20 21 -175.82 152.40 -35.00
3 3948 3S 4L C N 24 26 -63.39 -70.70 7.53 0.73 -63.50 175.38 24.34
3 4L 4L N CA 26 27 143.42 141.60 -41.20
4 3949 4L 5L C N 32 34 -67.90 -70.70 3.75 0.24 -63.50 179.75 25.21
4 5L 5L N CA 34 35 139.10 141.60 -41.20
5 3951 6I 7L C N 48 50 -81.18 -70.70 31.89 2.82 -63.50 153.71 20.39
5 7L 7L N CA 50 51 111.49 141.60 -41.20
6 3953 8V 9L C N 63 65 -115.37 -108.50 15.29 0.87 -63.50 168.23 21.02
6 9L 9L N CA 65 66 118.84 132.50 -41.20
7 3955 10C 11F C N 77 79 -164.64 -124.20 43.31 1.26 -63.20 -173.17 32.24
7 11F 11F N CA 79 80 158.81 143.30 -44.30
8 3956 11F 12L C N 88 90 -110.46 -108.50 36.70 2.00 -63.50 144.88 18.04
8 12L 12L N CA 90 91 95.86 132.50 -41.20
9 3958 13P 14L C N 103 105 -101.41 -108.50 8.08 0.43 -63.50 -178.43 23.32
9 14L 14L N CA 105 106 136.37 132.50 -41.20
10 3959 14L 15A C N 111 113 71.11 -68.20 140.32 12.44 -62.50 -153.83 31.40
10 15A 15A N CA 113 114 162.09 145.30 -40.90
11 3960 15A 16A C N 116 118 -149.88 -134.00 23.52 0.75 -62.50 177.72 33.79
11 16A 16A N CA 118 119 164.35 147.00 -40.90
12 3961 16A 17L C N 121 123 -79.03 -70.70 20.80 1.32 -63.50 158.90 22.98
12 17L 17L N CA 123 124 160.66 141.60 -41.20
13 3963 18G 19K C N 133 135 -119.23 -118.00 5.87 0.30 -62.90 -176.95 21.40
13 19K 19K N CA 135 136 133.36 139.10 -40.80
14 3998 53E 54S C N 410 412 -134.57 -64.10 78.27 8.19 -64.10 78.27 8.19
14 54S 54S N CA 412 413 -0.94 -35.00 -35.00
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 13 11 62 87 131 124 126 172 190 206
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 150
Number of all, selected real atoms : 1178 1178
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13203 13203
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2546
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 : 919.1730
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 : 1157 0 0 0.007 0.007 13.591 1.000
2 Bond angle potential : 1566 0 9 2.200 2.200 153.34 1.000
3 Stereochemical cosine torsion poten: 738 0 25 48.260 48.260 270.07 1.000
4 Stereochemical improper torsion pot: 468 0 0 1.435 1.435 21.667 1.000
5 Soft-sphere overlap restraints : 2546 1 2 0.008 0.008 17.197 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2404 0 0 0.109 0.109 35.255 1.000
10 Distance restraints 2 (N-O) : 2562 0 7 0.195 0.195 109.95 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: 146 0 2 4.476 4.476 34.494 1.000
14 Sidechain Chi_1 dihedral restraints: 120 0 2 75.229 75.229 34.411 1.000
15 Sidechain Chi_2 dihedral restraints: 86 0 0 78.011 78.011 42.145 1.000
16 Sidechain Chi_3 dihedral restraints: 29 0 0 84.810 84.810 16.847 1.000
17 Sidechain Chi_4 dihedral restraints: 18 0 0 96.973 96.973 11.871 1.000
18 Disulfide distance restraints : 4 0 0 0.006 0.006 0.23537E-01 1.000
19 Disulfide angle restraints : 8 0 0 2.748 2.748 1.3339 1.000
20 Disulfide dihedral angle restraints: 4 0 0 28.945 28.945 3.1684 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) : 1609 0 0 0.404 0.404 50.771 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: 145 15 11 20.269 58.646 27.209 1.000
26 Distance restraints 4 (SDCH-SDCH) : 738 0 0 0.772 0.772 64.649 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.028 0.028 11.187 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: plus_ligand.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: 15960.5449
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 3946 1M 2R C N 7 9 -76.55 -72.10 5.70 0.37 -63.00 173.96 24.42
1 2R 2R N CA 9 10 145.47 141.90 -41.10
2 3947 2R 3S C N 18 20 -149.48 -136.60 34.11 1.41 -64.10 165.87 18.17
2 3S 3S N CA 20 21 -177.22 151.20 -35.00
3 3948 3S 4L C N 24 26 -61.65 -70.70 9.61 0.75 -63.50 179.57 25.04
3 4L 4L N CA 26 27 138.36 141.60 -41.20
4 3949 4L 5L C N 32 34 -109.43 -108.50 1.79 0.10 -63.50 178.20 22.56
4 5L 5L N CA 34 35 130.98 132.50 -41.20
5 3951 6I 7L C N 48 50 -78.95 -70.70 16.74 1.57 -63.50 168.95 22.62
5 7L 7L N CA 50 51 127.04 141.60 -41.20
6 3953 8V 9L C N 63 65 -97.22 -108.50 31.81 1.58 -63.50 147.85 18.88
6 9L 9L N CA 65 66 102.75 132.50 -41.20
7 3955 10C 11F C N 77 79 -153.67 -124.20 30.01 1.01 -63.20 -170.32 32.10
7 11F 11F N CA 79 80 148.98 143.30 -44.30
8 3956 11F 12L C N 88 90 -106.33 -108.50 11.38 0.59 -63.50 168.08 21.29
8 12L 12L N CA 90 91 121.33 132.50 -41.20
9 3959 14L 15A C N 111 113 -123.71 -134.00 13.28 0.36 -62.50 -170.35 28.77
9 15A 15A N CA 113 114 138.60 147.00 -40.90
10 3960 15A 16A C N 116 118 -77.51 -68.20 10.54 0.72 -62.50 169.52 28.54
10 16A 16A N CA 118 119 150.25 145.30 -40.90
11 3961 16A 17L C N 121 123 -74.05 -70.70 7.14 0.44 -63.50 171.22 24.39
11 17L 17L N CA 123 124 147.91 141.60 -41.20
12 3963 18G 19K C N 133 135 -127.53 -118.00 10.58 0.35 -62.90 -172.97 28.15
12 19K 19K N CA 135 136 143.69 139.10 -40.80
13 3998 53E 54S C N 410 412 -138.53 -64.10 84.66 8.59 -64.10 84.66 8.59
13 54S 54S N CA 412 413 5.34 -35.00 -35.00
14 4032 87T 88P C N 684 686 -46.08 -58.70 56.63 3.76 -64.50 128.43 10.58
14 88P 88P N CA 686 687 -85.70 -30.50 147.20
15 4033 88P 89G C N 691 693 -64.33 -62.40 24.57 3.58 82.20 148.69 10.78
15 89G 89G N CA 693 694 -16.71 -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 7 57 86 111 126 148 169 186 216
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
plus_ligand.B99990001.pdb 888.73981
plus_ligand.B99990002.pdb 919.17297
In [5]:
#nglview.show_structure_file('plus_ligand.B99990001.pdb')
Image(filename = "/Users/Nataliyadi/Downloads/6hw/4.png", width=500, height=500)
Out[5]:
In [4]:
#nglview.show_structure_file('plus_ligand.B99990002.pdb')
Image(filename = "/Users/Nataliyadi/Downloads/6hw/5.png", width=500, height=500)
Out[4]:
Остался открытым вопрос, зачем нужно было использовать две модели, вероятно, хватило бы и одной. Особенно ввиду того, что не нужно выбирать лучшую из них.