Практикум 8. Гомологичное моделирование комплекса белка с лигандом¶
Зарегистрировался в Modeller, получил лицензию.
In [1]:
import sys
import modeller
import _modeller
import modeller.automodel
In [3]:
env=modeller.environ()
env.io.hetatm=True
Загрузим шаблон (белок форели)
In [4]:
! wget http://www.pdb.org/pdb/files/1lmp.pdb
--2020-05-19 10:15:02-- http://www.pdb.org/pdb/files/1lmp.pdb Resolving www.pdb.org (www.pdb.org)... 128.6.244.52 Connecting to www.pdb.org (www.pdb.org)|128.6.244.52|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://www.rcsb.org/pdb/files/1lmp.pdb [following] --2020-05-19 10:15:03-- https://www.rcsb.org/pdb/files/1lmp.pdb Resolving www.rcsb.org (www.rcsb.org)... 128.6.244.65 Connecting to www.rcsb.org (www.rcsb.org)|128.6.244.65|:443... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: http://files.rcsb.org/view/1lmp.pdb [following] --2020-05-19 10:15:03-- http://files.rcsb.org/view/1lmp.pdb Resolving files.rcsb.org (files.rcsb.org)... 128.6.244.12 Connecting to files.rcsb.org (files.rcsb.org)|128.6.244.12|:80... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/plain] Saving to: ‘1lmp.pdb’ 1lmp.pdb [ <=> ] 127.35K 317KB/s in 0.4s 2020-05-19 10:15:04 (317 KB/s) - ‘1lmp.pdb’ saved [130410]
И последовательность (я выбрал LYS_TRINI)
In [5]:
! wget http://www.uniprot.org/uniprot/P50718.fasta
URL transformed to HTTPS due to an HSTS policy --2020-05-19 10:15:12-- https://www.uniprot.org/uniprot/P50718.fasta Resolving www.uniprot.org (www.uniprot.org)... 128.175.245.202, 193.62.192.81 Connecting to www.uniprot.org (www.uniprot.org)|128.175.245.202|:443... connected. HTTP request sent, awaiting response... 200 Length: 211 [text/plain] Saving to: ‘P50718.fasta’ P50718.fasta 100%[===================>] 211 --.-KB/s in 0s 2020-05-19 10:15:28 (31.6 MB/s) - ‘P50718.fasta’ saved [211/211]
Построим выравнивание
In [42]:
alignm=modeller.alignment(env)
In [43]:
alignm.append(file='P50718.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')
## добавим идентификаторы
alignm[0].code = 'TRINI'
alignm[1].code = 'source'
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 [44]:
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
Смотрим, все ли ок?
In [45]:
! cat all_in_one.ali
>P1;TRINI sequence:: : : : :::-1.00:-1.00 MQKLRVFLLALAALCISCEAKYFATNCELVHELRRQGFPEDKMRDWVCLIQNESGRNTSKMGTINKNGSRDYGLF QINDKYWCSKTSTPGKD--CNVTCAEMLLDDITKASKCAKKI-YKRHKFQAWYGWRNHCQGTLPDISKC------ -* >P1;source 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 KVYDRCELA------------------RALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNR-NTDGSTDYGIF QINSRYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV.. .*
На первый взгляд, белки вовсе не похожи. На второй взгляд, в них есть (совсем небольшое) сходство, как, например, DDIT -> DDLT
In [46]:
## 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()
TRINI source
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
----------------------------------------------
92 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: 11787 10783
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 : 141
Number of all, selected real atoms : 1135 1135
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10783 10783
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2375
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 : 1110.8192
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 : 1158 0 0 0.008 0.008 19.880 1.000
2 Bond angle potential : 1555 1 8 2.358 2.358 172.26 1.000
3 Stereochemical cosine torsion poten: 730 0 27 47.680 47.680 265.13 1.000
4 Stereochemical improper torsion pot: 471 0 0 1.467 1.467 20.923 1.000
5 Soft-sphere overlap restraints : 2375 0 0 0.004 0.004 3.7305 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 0.411 0.411 124.07 1.000
10 Distance restraints 2 (N-O) : 2375 0 6 0.433 0.433 153.12 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: 140 2 4 5.395 5.395 48.056 1.000
14 Sidechain Chi_1 dihedral restraints: 124 0 3 78.040 78.040 54.292 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 1 72.520 72.520 40.623 1.000
16 Sidechain Chi_3 dihedral restraints: 42 0 0 82.760 82.760 31.683 1.000
17 Sidechain Chi_4 dihedral restraints: 23 0 0 81.770 81.770 18.653 1.000
18 Disulfide distance restraints : 3 0 0 0.019 0.019 0.18913 1.000
19 Disulfide angle restraints : 6 0 0 2.496 2.496 0.82566 1.000
20 Disulfide dihedral angle restraints: 3 0 0 26.475 26.475 2.0113 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) : 1244 0 0 0.424 0.424 27.224 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: 139 16 22 32.362 66.576 97.383 1.000
26 Distance restraints 4 (SDCH-SDCH) : 459 0 0 0.708 0.708 30.761 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: TRINI.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: 17400.6836
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 2164 92D 92D N CA 731 732 123.45 107.00 16.45 4.73 107.00 16.45 4.73
-------------------------------------------------------------------------------------------------
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 4092 27C 27C CA C 204 207 -157.24 -180.00 22.76 4.55 -180.00 22.76 4.55
2 4103 38F 38F CA C 296 304 -156.40 -180.00 23.60 4.72 -180.00 23.60 4.72
-------------------------------------------------------------------------------------------------
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 3935 9L 10A C N 78 80 -154.30 -134.00 55.24 2.52 -62.50 151.67 29.67
1 10A 10A N CA 80 81 -161.63 147.00 -40.90
2 3936 10A 11L C N 83 85 -64.28 -70.70 13.00 1.22 -63.50 165.89 23.08
2 11L 11L N CA 85 86 152.91 141.60 -41.20
3 3937 11L 12A C N 91 93 177.67 -134.00 50.91 1.20 -62.50 -163.20 38.53
3 12A 12A N CA 93 94 162.99 147.00 -40.90
4 3938 12A 13A C N 96 98 -78.37 -68.20 10.78 0.79 -62.50 170.96 28.82
4 13A 13A N CA 98 99 148.88 145.30 -40.90
5 3939 13A 14L C N 101 103 -101.35 -108.50 7.39 0.33 -63.50 175.96 22.55
5 14L 14L N CA 103 104 130.64 132.50 -41.20
6 3940 14L 15C C N 109 111 -67.29 -63.00 7.65 1.25 -117.90 178.78 7.67
6 15C 15C N CA 111 112 -47.43 -41.10 141.10
7 3944 18C 19E C N 135 137 146.23 -117.80 96.34 3.74 -63.60 -134.20 26.57
7 19E 19E N CA 137 138 128.33 136.80 -40.30
8 3945 19E 20A C N 144 146 -74.03 -68.20 14.52 0.97 -62.50 160.92 26.95
8 20A 20A N CA 146 147 158.60 145.30 -40.90
9 3946 20A 21K C N 149 151 95.27 56.60 130.94 12.36 -62.90 -138.19 27.04
9 21K 21K N CA 151 152 163.70 38.60 -40.80
10 3947 21K 22Y C N 158 160 -77.06 -98.40 22.49 1.05 -63.50 179.41 27.78
10 22Y 22Y N CA 160 161 135.50 128.40 -43.40
11 3949 23F 24A C N 181 183 -54.10 -68.20 14.30 1.13 -62.50 176.43 28.51
11 24A 24A N CA 183 184 142.87 145.30 -40.90
12 3950 24A 25T C N 186 188 -151.26 -124.80 54.37 1.71 -63.20 154.47 25.33
12 25T 25T N CA 188 189 -169.01 143.50 -42.10
13 3951 25T 26N C N 193 195 -123.89 -119.90 58.93 2.58 -63.20 137.25 20.58
13 26N 26N N CA 195 196 -164.20 137.00 -41.10
14 4011 85K 86T C N 689 691 78.50 55.90 42.68 2.09 -124.80 -149.73 12.69
14 86T 86T N CA 691 692 3.29 39.50 143.50
15 4017 91K 92D C N 729 731 -131.09 -63.30 71.41 12.08 -63.30 71.41 12.08
15 92D 92D N CA 731 732 -62.47 -40.00 -40.00
16 4041 115I 116Y C N 906 908 -45.44 -98.40 53.01 2.09 -63.50 170.41 27.97
16 116Y 116Y N CA 908 909 126.05 128.40 -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 12 10 56 77 128 134 129 166 182 189
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 141
Number of all, selected real atoms : 1135 1135
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10783 10783
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2341
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 : 1187.9681
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 : 1158 0 1 0.008 0.008 18.913 1.000
2 Bond angle potential : 1555 1 12 2.276 2.276 160.68 1.000
3 Stereochemical cosine torsion poten: 730 0 30 47.225 47.225 258.94 1.000
4 Stereochemical improper torsion pot: 471 0 0 1.313 1.313 17.460 1.000
5 Soft-sphere overlap restraints : 2341 0 0 0.004 0.004 3.3868 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 0.416 0.416 130.73 1.000
10 Distance restraints 2 (N-O) : 2375 0 17 0.537 0.537 219.02 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: 140 1 5 5.752 5.752 54.622 1.000
14 Sidechain Chi_1 dihedral restraints: 124 0 1 72.746 72.746 31.501 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 0 78.977 78.977 34.884 1.000
16 Sidechain Chi_3 dihedral restraints: 42 0 0 85.507 85.507 31.287 1.000
17 Sidechain Chi_4 dihedral restraints: 23 0 1 103.296 103.296 20.720 1.000
18 Disulfide distance restraints : 3 0 0 0.017 0.017 0.15622 1.000
19 Disulfide angle restraints : 6 0 0 2.017 2.017 0.53880 1.000
20 Disulfide dihedral angle restraints: 3 0 0 33.550 33.550 3.1733 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) : 1244 0 0 0.458 0.458 25.523 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: 139 25 28 33.539 75.257 145.65 1.000
26 Distance restraints 4 (SDCH-SDCH) : 459 0 0 0.700 0.700 30.781 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: TRINI.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: 17838.3008
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 2164 92D 92D N CA 731 732 123.93 107.00 16.93 4.87 107.00 16.93 4.87
-------------------------------------------------------------------------------------------------
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 4103 38F 38F CA C 296 304 -156.65 -180.00 23.35 4.67 -180.00 23.35 4.67
-------------------------------------------------------------------------------------------------
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 3929 3K 4L C N 25 27 -65.97 -63.50 15.67 2.32 -70.70 161.80 12.44
1 4L 4L N CA 27 28 -56.67 -41.20 141.60
2 3930 4L 5R C N 33 35 160.03 -63.00 141.02 25.00 -63.00 141.02 25.00
2 5R 5R N CA 35 36 -74.65 -41.10 -41.10
3 3935 9L 10A C N 78 80 162.18 -134.00 64.35 1.84 -62.50 -147.43 41.87
3 10A 10A N CA 80 81 155.18 147.00 -40.90
4 3936 10A 11L C N 83 85 -161.31 -108.50 55.52 2.48 -63.50 -164.60 33.15
4 11L 11L N CA 85 86 149.63 132.50 -41.20
5 3937 11L 12A C N 91 93 -69.81 -68.20 1.62 0.13 -62.50 173.82 28.85
5 12A 12A N CA 93 94 145.44 145.30 -40.90
6 3938 12A 13A C N 96 98 -91.75 -68.20 41.98 4.07 -62.50 154.26 24.02
6 13A 13A N CA 98 99 110.56 145.30 -40.90
7 3944 18C 19E C N 135 137 -71.27 -69.30 5.05 0.31 -63.60 172.72 23.45
7 19E 19E N CA 137 138 147.15 142.50 -40.30
8 3945 19E 20A C N 144 146 93.90 -134.00 132.13 4.47 -62.50 -125.69 35.84
8 20A 20A N CA 146 147 144.63 147.00 -40.90
9 3946 20A 21K C N 149 151 -115.89 -118.00 31.59 1.50 -62.90 157.56 18.31
9 21K 21K N CA 151 152 107.59 139.10 -40.80
10 3948 22Y 23F C N 170 172 -143.04 -124.20 33.34 1.02 -63.20 165.44 28.04
10 23F 23F N CA 172 173 170.80 143.30 -44.30
11 3950 24A 25T C N 186 188 -138.05 -124.80 17.19 0.58 -63.20 179.77 27.95
11 25T 25T N CA 188 189 154.45 143.50 -42.10
12 3951 25T 26N C N 193 195 -137.49 -119.90 19.83 1.02 -63.20 -175.43 20.04
12 26N 26N N CA 195 196 127.86 137.00 -41.10
13 3953 27C 28E C N 207 209 -69.51 -63.60 65.18 9.02 -63.60 65.18 9.02
13 28E 28E N CA 209 210 -105.21 -40.30 -40.30
14 3961 35R 36Q C N 280 282 -57.04 -63.80 8.72 1.16 -121.10 -174.13 9.61
14 36Q 36Q N CA 282 283 -45.81 -40.30 139.70
15 3962 36Q 37G C N 289 291 -87.01 -62.40 27.91 4.30 82.20 173.11 12.74
15 37G 37G N CA 291 292 -28.03 -41.20 8.50
16 3979 53E 54S C N 433 435 -138.59 -64.10 82.00 8.69 -64.10 82.00 8.69
16 54S 54S N CA 435 436 -0.72 -35.00 -35.00
17 3989 63T 64I C N 503 505 -63.79 -63.40 4.56 0.73 -120.60 178.64 8.15
17 64I 64I N CA 505 506 -39.06 -43.60 130.30
18 3992 66K 67N C N 528 530 -68.23 -119.90 64.83 3.46 -63.20 142.82 18.13
18 67N 67N N CA 530 531 176.17 137.00 -41.10
19 3993 67N 68G C N 536 538 -60.15 -62.40 14.53 2.29 82.20 146.67 10.90
19 68G 68G N CA 538 539 -26.85 -41.20 8.50
20 4011 85K 86T C N 689 691 74.01 55.90 38.70 1.85 -124.80 -147.68 12.83
20 86T 86T N CA 691 692 5.30 39.50 143.50
21 4017 91K 92D C N 729 731 161.38 -96.50 103.43 4.21 -63.30 -166.87 21.74
21 92D 92D N CA 731 732 97.80 114.20 -40.00
22 4042 116Y 117K C N 918 920 -58.06 -62.90 12.55 1.45 -118.00 178.86 9.22
22 117K 117K N CA 920 921 -52.38 -40.80 139.10
23 4043 117K 118R C N 927 929 -73.38 -125.20 82.52 4.57 -63.00 114.56 16.18
23 118R 118R N CA 929 930 -155.18 140.60 -41.10
24 4044 118R 119H C N 938 940 -54.96 -125.60 77.30 2.08 -63.20 149.93 19.26
24 119H 119H N CA 940 941 107.40 138.80 -42.30
25 4045 119H 120K C N 948 950 -41.73 -62.90 75.74 8.91 -118.00 131.71 6.78
25 120K 120K N CA 950 951 -113.52 -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 16 10 62 72 116 106 144 156 196 175
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
TRINI.B99990001.pdb 1110.81921
TRINI.B99990002.pdb 1187.96814
Вывод был длинный... посмотрим лучше на результат!
In [48]:
import nglview
import ipywidgets
w1 = nglview.show_structure_file('TRINI_L.B99990001.pdb')
w1
--------------------------------------------------------------------------- ModuleNotFoundError Traceback (most recent call last) <ipython-input-48-03c377c37665> in <module> ----> 1 import nglview 2 import ipywidgets 3 w1 = nglview.show_structure_file('TRINI_L.B99990001.pdb') 4 w1 ModuleNotFoundError: No module named 'nglview'
И опять nglview умер. Проще в pymol.
In [49]:
from IPython.display import display, Image
In [50]:
import __main__
__main__.pymol_argv = [ 'pymol', '-x' ]
import pymol
pymol.finish_launching()
from pymol import cmd, stored
In [51]:
cmd.load('TRINI.B99990001.pdb', 'model1')
cmd.load('1lmp.pdb', 'source')
cmd.do('align model1, source')
cmd.do('remove hetatm')
cmd.bg_color('white')
cmd.set('ray_trace_mode', 3)
In [52]:
cmd.do('ray; png 1+2.png')
In [53]:
Image('1+2.png')
Out[53]:
Добавим лиганд в целевой белок (мы помним, что он был проигнорирован modeller'ом)
In [51]:
seq = ''
for res in alignm[0].residues:
seq += res.code
for lig in alignm[1].residues[-3:]:
seq += lig.code
seq
Out[51]:
'MQKLRVFLLALAALCISCEAKYFATNCELVHELRRQGFPEDKMRDWVCLIQNESGRNTSKMGTINKNGSRDYGLFQINDKYWCSKTSTPGKDCNVTCAEMLLDDITKASKCAKKIYKRHKFQAWYGWRNHCQGTLPDISKC...'
In [65]:
alignm.append_sequence(seq)
alignm[2].code = 'TRINI_L'
In [66]:
del alignm[0]
In [67]:
alignm.salign()
alignm.write(file='all_in_one2.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [68]:
! cat all_in_one2.ali
>P1;source 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 KVYDRCELA------------------RALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNR-NTDGSTDYGIF QINSRYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV.. .* >P1;TRINI_L sequence::1 : :+144 : :undefined:undefined:-1.00:-1.00 MQKLRVFLLALAALCISCEAKYFATNCELVHELRRQGFPEDKMRDWVCLIQNESGRNTSKMGTINKNGSRDYGLF QINDKYWCSKTSTPGKD--CNVTCAEMLLDDITKASKCAKKI-YKRHKFQAWYGWRNHCQG----TLPDISKC.. .*
Почему-то выравнивание не отображается в текстовом виде...
Иии... смоделируем
In [69]:
## 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_one2.ali', knowns=pdb.code, sequence=s.code)
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
TRINI_L source
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
----------------------------------------------
92 1 73 76 D C 8.895
136 1 117 122 G T 13.814
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 141
atom names : C +N
atom indices : 1133 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 141
atom names : C CA +N O
atom indices : 1133 1130 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: 3
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/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: 13130 12126
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 : 144
Number of all, selected real atoms : 1178 1178
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12126 12126
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2688
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 : 1343.8245
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 : 1158 0 1 0.009 0.009 27.082 1.000
2 Bond angle potential : 1555 1 14 2.464 2.464 184.10 1.000
3 Stereochemical cosine torsion poten: 730 0 36 49.260 49.260 275.88 1.000
4 Stereochemical improper torsion pot: 471 0 0 1.368 1.368 18.697 1.000
5 Soft-sphere overlap restraints : 2688 1 2 0.008 0.008 20.804 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) : 2202 0 10 0.525 0.525 187.87 1.000
10 Distance restraints 2 (N-O) : 2360 0 9 0.546 0.546 202.00 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: 140 1 4 5.522 5.522 50.335 1.000
14 Sidechain Chi_1 dihedral restraints: 124 0 1 81.462 81.462 41.113 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 2 76.560 76.560 46.972 1.000
16 Sidechain Chi_3 dihedral restraints: 42 0 0 73.171 73.171 25.990 1.000
17 Sidechain Chi_4 dihedral restraints: 23 0 0 84.045 84.045 15.362 1.000
18 Disulfide distance restraints : 3 0 0 0.023 0.023 0.27114 1.000
19 Disulfide angle restraints : 6 0 0 2.295 2.295 0.69808 1.000
20 Disulfide dihedral angle restraints: 3 0 0 39.773 39.773 2.9675 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) : 1225 0 0 0.462 0.462 25.248 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: 139 22 30 34.297 71.546 148.36 1.000
26 Distance restraints 4 (SDCH-SDCH) : 462 0 0 0.825 0.825 41.686 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.050 0.050 28.387 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: TRINI_L.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: 18801.0586
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 2164 92D 92D N CA 731 732 123.55 107.00 16.55 4.76 107.00 16.55 4.76
-------------------------------------------------------------------------------------------------
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 4103 38F 38F CA C 296 304 -155.92 -180.00 24.08 4.81 -180.00 24.08 4.81
-------------------------------------------------------------------------------------------------
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 3935 9L 10A C N 78 80 19.89 -68.20 89.39 8.06 -62.50 178.72 26.78
1 10A 10A N CA 80 81 160.50 145.30 -40.90
2 3936 10A 11L C N 83 85 -164.88 -108.50 60.12 2.68 -63.50 -165.99 33.16
2 11L 11L N CA 85 86 153.38 132.50 -41.20
3 3937 11L 12A C N 91 93 -66.50 -68.20 2.40 0.24 -62.50 172.15 28.41
3 12A 12A N CA 93 94 147.00 145.30 -40.90
4 3938 12A 13A C N 96 98 -114.23 -134.00 20.97 0.49 -62.50 -173.58 33.30
4 13A 13A N CA 98 99 140.01 147.00 -40.90
5 3939 13A 14L C N 101 103 -76.78 -70.70 7.52 0.76 -63.50 178.88 24.11
5 14L 14L N CA 103 104 137.18 141.60 -41.20
6 3942 16I 17S C N 123 125 -168.38 -136.60 32.66 1.11 -64.10 -163.73 21.74
6 17S 17S N CA 125 126 158.72 151.20 -35.00
7 3944 18C 19E C N 135 137 -173.25 -117.80 72.72 2.24 -63.60 174.57 29.10
7 19E 19E N CA 137 138 -176.14 136.80 -40.30
8 3945 19E 20A C N 144 146 -72.18 -68.20 11.08 0.76 -62.50 163.74 27.32
8 20A 20A N CA 146 147 155.65 145.30 -40.90
9 3947 21K 22Y C N 158 160 -132.35 -124.30 9.07 0.75 -63.50 -172.30 26.71
9 22Y 22Y N CA 160 161 131.22 135.40 -43.40
10 3948 22Y 23F C N 170 172 -160.31 -124.20 37.00 1.67 -63.20 -155.86 23.28
10 23F 23F N CA 172 173 135.26 143.30 -44.30
11 3949 23F 24A C N 181 183 -115.13 -134.00 63.56 3.07 -62.50 137.66 20.73
11 24A 24A N CA 183 184 86.30 147.00 -40.90
12 3953 27C 28E C N 207 209 -77.55 -63.60 57.01 8.39 -63.60 57.01 8.39
12 28E 28E N CA 209 210 -95.58 -40.30 -40.30
13 3979 53E 54S C N 433 435 -135.92 -64.10 78.55 8.40 -64.10 78.55 8.40
13 54S 54S N CA 435 436 -3.17 -35.00 -35.00
14 3989 63T 64I C N 503 505 -63.46 -63.40 13.36 2.19 -120.60 170.41 7.69
14 64I 64I N CA 505 506 -30.24 -43.60 130.30
15 4011 85K 86T C N 689 691 80.44 55.90 50.67 2.43 -124.80 -145.64 12.89
15 86T 86T N CA 691 692 -4.82 39.50 143.50
16 4017 91K 92D C N 729 731 -133.11 -63.30 79.63 13.60 -63.30 79.63 13.60
16 92D 92D N CA 731 732 -78.32 -40.00 -40.00
17 4041 115I 116Y C N 906 908 -47.61 -98.40 56.14 3.39 -63.50 148.74 24.42
17 116Y 116Y N CA 908 909 104.49 128.40 -43.40
18 4058 132Q 133G C N 1070 1072 128.37 78.70 53.76 2.06 82.20 171.17 10.53
18 133G 133G N CA 1072 1073 173.33 -166.10 8.50
19 4059 133G 134T C N 1074 1076 -113.29 -124.80 38.53 1.33 -63.20 157.03 17.34
19 134T 134T N CA 1076 1077 106.73 143.50 -42.10
20 4062 136P 137D C N 1096 1098 36.78 -70.90 123.14 10.33 -63.30 148.69 16.51
20 137D 137D N CA 1098 1099 -149.96 150.30 -40.00
21 4064 138I 139S C N 1112 1114 -127.30 -136.60 62.84 2.98 -64.10 139.22 8.90
21 139S 139S N CA 1114 1115 89.05 151.20 -35.00
22 4065 139S 140K C N 1118 1120 -34.80 -70.20 51.93 3.11 -62.90 145.94 20.59
22 140K 140K N CA 1120 1121 102.41 140.40 -40.80
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 16 16 78 82 154 149 158 185 198 219
<< 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 : 144
Number of all, selected real atoms : 1178 1178
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12126 12126
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2643
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 : 1508.3385
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 : 1158 0 1 0.010 0.010 33.667 1.000
2 Bond angle potential : 1555 1 15 2.615 2.615 211.27 1.000
3 Stereochemical cosine torsion poten: 730 0 34 49.325 49.325 280.90 1.000
4 Stereochemical improper torsion pot: 471 0 1 1.661 1.661 27.145 1.000
5 Soft-sphere overlap restraints : 2643 1 2 0.009 0.009 25.992 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) : 2202 0 11 0.550 0.550 227.00 1.000
10 Distance restraints 2 (N-O) : 2360 0 13 0.569 0.569 242.70 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 140 3 7 6.685 6.685 73.777 1.000
14 Sidechain Chi_1 dihedral restraints: 124 0 3 73.368 73.368 52.767 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 0 77.700 77.700 49.639 1.000
16 Sidechain Chi_3 dihedral restraints: 42 0 0 83.973 83.973 30.384 1.000
17 Sidechain Chi_4 dihedral restraints: 23 0 0 91.802 91.802 16.301 1.000
18 Disulfide distance restraints : 3 0 0 0.023 0.023 0.28187 1.000
19 Disulfide angle restraints : 6 0 0 4.439 4.439 2.6108 1.000
20 Disulfide dihedral angle restraints: 3 0 0 11.344 11.344 0.45829 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) : 1225 0 0 0.443 0.443 28.988 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: 139 22 25 28.993 72.752 128.61 1.000
26 Distance restraints 4 (SDCH-SDCH) : 462 0 2 0.857 0.857 43.753 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.053 0.053 32.095 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: TRINI_L.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: 20105.7207
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 2164 92D 92D N CA 731 732 124.35 107.00 17.35 4.99 107.00 17.35 4.99
-------------------------------------------------------------------------------------------------
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 4103 38F 38F CA C 296 304 -156.66 -180.00 23.34 4.67 -180.00 23.34 4.67
-------------------------------------------------------------------------------------------------
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 3935 9L 10A C N 78 80 -127.39 -134.00 8.69 0.49 -62.50 178.67 32.75
1 10A 10A N CA 80 81 152.63 147.00 -40.90
2 3936 10A 11L C N 83 85 -75.82 -70.70 10.40 0.98 -63.50 174.19 23.51
2 11L 11L N CA 85 86 132.55 141.60 -41.20
3 3937 11L 12A C N 91 93 -124.77 -134.00 24.66 1.12 -62.50 176.38 26.65
3 12A 12A N CA 93 94 124.13 147.00 -40.90
4 3938 12A 13A C N 96 98 -166.25 -134.00 33.28 0.83 -62.50 -166.03 37.30
4 13A 13A N CA 98 99 155.22 147.00 -40.90
5 3939 13A 14L C N 101 103 -92.31 -108.50 28.07 1.31 -63.50 153.50 19.85
5 14L 14L N CA 103 104 109.57 132.50 -41.20
6 3942 16I 17S C N 123 125 -173.49 -136.60 36.89 1.47 -64.10 -154.47 22.78
6 17S 17S N CA 125 126 150.99 151.20 -35.00
7 3944 18C 19E C N 135 137 -101.94 -117.80 39.45 1.61 -63.60 146.10 17.66
7 19E 19E N CA 137 138 100.68 136.80 -40.30
8 3946 20A 21K C N 149 151 -71.69 -70.20 13.12 0.92 -62.90 166.00 22.05
8 21K 21K N CA 151 152 153.44 140.40 -40.80
9 3947 21K 22Y C N 158 160 -75.41 -98.40 25.20 1.33 -63.50 178.27 28.90
9 22Y 22Y N CA 160 161 138.72 128.40 -43.40
10 3948 22Y 23F C N 170 172 -108.25 -124.20 15.98 0.65 -63.20 177.31 27.64
10 23F 23F N CA 172 173 144.21 143.30 -44.30
11 3949 23F 24A C N 181 183 -123.69 -134.00 18.54 1.13 -62.50 168.21 30.84
11 24A 24A N CA 183 184 162.41 147.00 -40.90
12 3950 24A 25T C N 186 188 -53.01 -78.10 32.25 1.28 -63.20 171.94 22.72
12 25T 25T N CA 188 189 129.54 149.80 -42.10
13 3951 25T 26N C N 193 195 -128.88 -119.90 14.03 0.42 -63.20 -176.71 26.65
13 26N 26N N CA 195 196 147.78 137.00 -41.10
14 3956 30V 31H C N 231 233 179.15 -125.60 68.31 3.04 -63.20 -176.41 20.05
14 31H 31H N CA 233 234 98.64 138.80 -42.30
15 4011 85K 86T C N 689 691 80.06 55.90 51.03 2.44 -124.80 -144.93 12.93
15 86T 86T N CA 691 692 -5.45 39.50 143.50
16 4017 91K 92D C N 729 731 -141.51 -63.30 84.90 14.46 -63.30 84.90 14.46
16 92D 92D N CA 731 732 -73.02 -40.00 -40.00
17 4041 115I 116Y C N 906 908 -45.66 -98.40 57.61 3.38 -63.50 149.69 24.67
17 116Y 116Y N CA 908 909 105.22 128.40 -43.40
18 4044 118R 119H C N 938 940 -89.40 -125.60 50.92 1.26 -63.20 147.63 16.98
18 119H 119H N CA 940 941 102.98 138.80 -42.30
19 4058 132Q 133G C N 1070 1072 135.13 78.70 58.77 2.48 82.20 177.05 11.12
19 133G 133G N CA 1072 1073 177.46 -166.10 8.50
20 4059 133G 134T C N 1074 1076 -108.79 -124.80 40.01 1.30 -63.20 155.76 17.37
20 134T 134T N CA 1076 1077 106.83 143.50 -42.10
21 4062 136P 137D C N 1096 1098 46.35 -70.90 128.36 10.75 -63.30 160.69 17.92
21 137D 137D N CA 1098 1099 -157.46 150.30 -40.00
22 4065 139S 140K C N 1118 1120 58.79 56.60 9.26 0.83 -62.90 150.41 26.11
22 140K 140K N CA 1120 1121 47.59 38.60 -40.80
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 1 12 25 81 82 125 137 171 182 181 186
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
TRINI_L.B99990001.pdb 1343.82446
TRINI_L.B99990002.pdb 1508.33850
In [70]:
cmd.reinitialize()
In [71]:
cmd.load('TRINI_L.B99990001.pdb', 'model1')
cmd.load('1lmp.pdb', 'source')
cmd.do('align model1, source')
cmd.bg_color('white')
cmd.set('ray_trace_mode', 3)
In [72]:
cmd.do('ray; png 2+2.png')
In [74]:
display(Image('1+2.png'), Image('2+2.png'))
Как видим, в обоих случаях совпадение структуры наблюдается, а выравнивания просто совершенно не похожи! Вывод - modeller просто подгоняет сиквенс под известную структуру без учета сворачивания белка (что довольно логично и мы и так знали, да и вычисления тут небольшие).
Добавим случайный шум к положению лиганда
In [ ]:
In [78]:
class mymodel(modeller.automodel.automodel):
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
for x,y in [('N:50','O6:142'), ('N:70', 'O6:144')]:
rsr.add(modeller.forms.gaussian(group=modeller.physical.xy_distance,
feature=modeller.features.distance(
at[x],at[y]),mean=3.0, stdev=0.1))
In [80]:
a = mymodel(env, alnfile='all_in_one2.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
----------------------------------------------
92 1 73 76 D C 8.895
136 1 117 122 G T 13.814
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 141
atom names : C +N
atom indices : 1133 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 141
atom names : C CA +N O
atom indices : 1133 1130 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: 3
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/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: 13132 12128
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 : 144
Number of all, selected real atoms : 1178 1178
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12128 12128
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2706
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 : 5646.9092
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 : 1158 5 9 0.020 0.020 135.99 1.000
2 Bond angle potential : 1555 9 29 3.457 3.457 364.02 1.000
3 Stereochemical cosine torsion poten: 730 0 33 48.704 48.704 273.61 1.000
4 Stereochemical improper torsion pot: 471 0 0 1.510 1.510 25.303 1.000
5 Soft-sphere overlap restraints : 2706 3 4 0.011 0.011 36.583 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) : 2202 17 64 0.700 0.700 700.32 1.000
10 Distance restraints 2 (N-O) : 2360 10 45 0.659 0.659 573.17 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: 140 3 11 8.341 8.341 114.87 1.000
14 Sidechain Chi_1 dihedral restraints: 124 0 2 81.648 81.648 51.050 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 0 69.350 69.350 35.709 1.000
16 Sidechain Chi_3 dihedral restraints: 42 0 0 80.685 80.685 30.183 1.000
17 Sidechain Chi_4 dihedral restraints: 23 0 0 113.894 113.894 18.334 1.000
18 Disulfide distance restraints : 3 0 0 0.024 0.024 0.29598 1.000
19 Disulfide angle restraints : 6 0 0 3.464 3.464 1.5901 1.000
20 Disulfide dihedral angle restraints: 3 0 0 18.651 18.651 1.0955 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) : 1225 0 0 0.442 0.442 34.979 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: 139 27 35 36.546 76.607 204.03 1.000
26 Distance restraints 4 (SDCH-SDCH) : 462 1 3 1.118 1.118 90.681 1.000
27 Distance restraints 5 (X-Y) : 1391 19 75 0.332 0.332 2955.1 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: TRINI_L.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: 24889.5391
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 1 : Bond length potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 413 50I 50I N CA 401 402 1.79 1.43 0.36 11.69 1.43 0.36 11.69
2 415 50I 50I C CA 407 402 1.75 1.49 0.26 7.46 1.49 0.26 7.46
3 554 69S 69S C CA 546 543 1.67 1.49 0.18 5.21 1.49 0.18 5.21
4 555 69S 70R C N 546 548 1.50 1.35 0.16 5.64 1.35 0.16 5.64
5 563 70R 70R N CA 548 549 1.64 1.43 0.21 7.07 1.43 0.21 7.07
-------------------------------------------------------------------------------------------------
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 1702 49L 49L N CA 393 394 127.74 107.00 20.74 5.96 107.00 20.74 5.96
2 1713 50I 50I N CA 401 402 141.11 107.00 34.11 9.81 107.00 34.11 9.81
3 1717 50I 50I CA C 402 407 134.89 116.50 18.39 5.29 116.50 18.39 5.29
4 1903 69S 69S CA C 543 546 137.94 116.50 21.44 6.17 116.50 21.44 6.17
5 2164 92D 92D N CA 731 732 123.24 107.00 16.24 4.67 107.00 16.24 4.67
-------------------------------------------------------------------------------------------------
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 4562 3K 50I CA CA 19 402 12.04 9.92 2.12 4.69 9.92 2.12 4.69
2 5381 50I 56R CA CA 402 446 7.66 5.65 2.01 6.51 5.65 2.01 6.51
-------------------------------------------------------------------------------------------------
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 7284 50I 5R N O 401 45 12.46 9.64 2.82 5.05 9.64 2.82 5.05
2 7285 50I 8L N O 401 71 12.07 9.87 2.21 4.55 9.87 2.21 4.55
3 7291 50I 47V N O 401 386 5.49 3.33 2.17 6.00 3.33 2.17 6.00
4 7311 50I 135L N O 401 1090 12.67 9.76 2.91 5.25 9.76 2.91 5.25
5 7445 56R 50I N O 445 408 4.93 3.48 1.45 4.58 3.48 1.45 4.58
-------------------------------------------------------------------------------------------------
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 4103 38F 38F CA C 296 304 -155.86 -180.00 24.14 4.83 -180.00 24.14 4.83
2 4134 69S 69S CA C 543 546 -132.26 -180.00 47.74 9.54 -180.00 47.74 9.54
-------------------------------------------------------------------------------------------------
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 3935 9L 10A C N 78 80 -166.35 -134.00 33.06 1.36 -62.50 -153.14 39.44
1 10A 10A N CA 80 81 140.20 147.00 -40.90
2 3936 10A 11L C N 83 85 -116.55 -108.50 36.84 1.90 -63.50 159.43 25.42
2 11L 11L N CA 85 86 168.46 132.50 -41.20
3 3937 11L 12A C N 91 93 -65.01 -68.20 12.15 1.09 -62.50 162.09 26.69
3 12A 12A N CA 93 94 157.03 145.30 -40.90
4 3938 12A 13A C N 96 98 -64.73 -68.20 9.25 0.86 -62.50 165.24 27.19
4 13A 13A N CA 98 99 153.88 145.30 -40.90
5 3939 13A 14L C N 101 103 -70.31 -70.70 19.33 1.48 -63.50 158.02 22.34
5 14L 14L N CA 103 104 160.93 141.60 -41.20
6 3940 14L 15C C N 109 111 -60.28 -63.00 2.73 0.45 -117.90 -173.19 8.06
6 15C 15C N CA 111 112 -41.20 -41.10 141.10
7 3942 16I 17S C N 123 125 -150.23 -136.60 31.44 1.25 -64.10 169.05 18.45
7 17S 17S N CA 125 126 179.53 151.20 -35.00
8 3944 18C 19E C N 135 137 -57.28 -69.30 17.50 0.98 -63.60 170.20 23.04
8 19E 19E N CA 137 138 129.78 142.50 -40.30
9 3945 19E 20A C N 144 146 -77.63 -68.20 11.57 0.75 -62.50 167.78 28.26
9 20A 20A N CA 146 147 152.00 145.30 -40.90
10 3946 20A 21K C N 149 151 -73.23 -70.20 18.86 1.44 -62.90 162.91 20.61
10 21K 21K N CA 151 152 121.78 140.40 -40.80
11 3949 23F 24A C N 181 183 -152.72 -134.00 19.58 0.47 -62.50 -170.77 35.83
11 24A 24A N CA 183 184 152.76 147.00 -40.90
12 3950 24A 25T C N 186 188 -77.96 -78.10 13.75 0.59 -63.20 155.06 20.86
12 25T 25T N CA 188 189 163.55 149.80 -42.10
13 3951 25T 26N C N 193 195 -115.05 -119.90 5.22 0.17 -63.20 -176.38 20.54
13 26N 26N N CA 195 196 135.05 137.00 -41.10
14 3974 48C 49L C N 391 393 -70.11 -63.50 58.69 8.54 -63.50 58.69 8.54
14 49L 49L N CA 393 394 -99.52 -41.20 -41.20
15 3975 49L 50I C N 399 401 -14.31 -63.40 49.09 8.77 -63.40 49.09 8.77
15 50I 50I N CA 401 402 -43.50 -43.60 -43.60
16 3989 63T 64I C N 503 505 -65.50 -63.40 10.18 1.60 -120.60 172.95 7.89
16 64I 64I N CA 505 506 -33.64 -43.60 130.30
17 4011 85K 86T C N 689 691 80.97 55.90 54.47 2.60 -124.80 -143.22 13.01
17 86T 86T N CA 691 692 -8.85 39.50 143.50
18 4017 91K 92D C N 729 731 -138.58 -63.30 82.74 14.11 -63.30 82.74 14.11
18 92D 92D N CA 731 732 -74.32 -40.00 -40.00
19 4043 117K 118R C N 927 929 -57.00 -125.20 68.22 2.77 -63.00 177.07 23.52
19 118R 118R N CA 929 930 141.94 140.60 -41.10
20 4044 118R 119H C N 938 940 115.65 -63.20 -179.90 29.52 -63.20 -179.90 29.52
20 119H 119H N CA 940 941 -21.06 -42.30 -42.30
21 4045 119H 120K C N 948 950 49.13 -62.90 141.70 18.06 -118.00 -168.58 8.97
21 120K 120K N CA 950 951 -127.57 -40.80 139.10
22 4055 129N 130H C N 1045 1047 -130.31 -63.20 77.25 9.82 -63.20 77.25 9.82
22 130H 130H N CA 1047 1048 -4.06 -42.30 -42.30
23 4058 132Q 133G C N 1070 1072 128.37 78.70 52.70 2.12 82.20 174.02 10.67
23 133G 133G N CA 1072 1073 176.29 -166.10 8.50
24 4059 133G 134T C N 1074 1076 -104.90 -124.80 37.93 1.18 -63.20 158.87 17.94
24 134T 134T N CA 1076 1077 111.20 143.50 -42.10
25 4062 136P 137D C N 1096 1098 39.89 -70.90 125.52 10.54 -63.30 151.35 16.87
25 137D 137D N CA 1098 1099 -150.71 150.30 -40.00
26 4064 138I 139S C N 1112 1114 -116.63 -136.60 48.99 1.98 -64.10 150.91 9.31
26 139S 139S N CA 1114 1115 106.47 151.20 -35.00
27 4065 139S 140K C N 1118 1120 -55.80 -70.20 36.59 2.32 -62.90 147.73 19.58
27 140K 140K N CA 1120 1121 106.76 140.40 -40.80
-------------------------------------------------------------------------------------------------
Feature 26 : Distance restraints 4 (SDCH-SDCH)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 10300 8L 50I CD2 CB 69 403 8.62 3.62 5.00 4.74 3.62 5.00 4.74
-------------------------------------------------------------------------------------------------
Feature 27 : Distance restraints 5 (X-Y)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 11694 142. 142. O4 O6 1146 1148 3.69 3.43 0.26 5.14 3.43 0.26 5.14
2 11719 142. 142. O6 O4 1148 1146 3.69 3.43 0.26 5.14 3.43 0.26 5.14
3 12127 50I 142. N O6 401 1148 10.26 3.00 7.26 72.63 3.00 7.26 72.63
4 12128 70R 144. N O6 548 1175 8.13 3.00 5.13 51.27 3.00 5.13 51.27
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 20 33 98 72 151 136 158 199 172 212
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 144
Number of all, selected real atoms : 1178 1178
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12128 12128
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2771
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 : 5820.8091
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 : 1158 5 9 0.020 0.020 143.21 1.000
2 Bond angle potential : 1555 7 30 3.522 3.522 377.30 1.000
3 Stereochemical cosine torsion poten: 730 0 39 50.628 50.628 296.71 1.000
4 Stereochemical improper torsion pot: 471 0 1 1.998 1.998 41.698 1.000
5 Soft-sphere overlap restraints : 2771 3 4 0.012 0.012 44.211 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) : 2202 16 69 0.715 0.715 708.00 1.000
10 Distance restraints 2 (N-O) : 2360 8 49 0.665 0.665 586.69 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 140 5 10 9.039 9.039 134.90 1.000
14 Sidechain Chi_1 dihedral restraints: 124 0 2 79.061 79.061 44.896 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 2 69.407 69.407 38.539 1.000
16 Sidechain Chi_3 dihedral restraints: 42 0 0 76.379 76.379 29.559 1.000
17 Sidechain Chi_4 dihedral restraints: 23 0 0 97.087 97.087 15.897 1.000
18 Disulfide distance restraints : 3 0 0 0.023 0.023 0.26643 1.000
19 Disulfide angle restraints : 6 0 0 2.200 2.200 0.64125 1.000
20 Disulfide dihedral angle restraints: 3 0 0 25.766 25.766 1.9957 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) : 1225 0 0 0.520 0.520 36.017 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: 139 29 30 36.369 79.762 206.77 1.000
26 Distance restraints 4 (SDCH-SDCH) : 462 0 8 1.148 1.148 91.123 1.000
27 Distance restraints 5 (X-Y) : 1391 19 80 0.336 0.336 3022.4 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: TRINI_L.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: 25668.7773
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 1 : Bond length potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 413 50I 50I N CA 401 402 1.79 1.43 0.36 11.75 1.43 0.36 11.75
2 415 50I 50I C CA 407 402 1.75 1.49 0.26 7.48 1.49 0.26 7.48
3 554 69S 69S C CA 546 543 1.66 1.49 0.17 5.04 1.49 0.17 5.04
4 555 69S 70R C N 546 548 1.52 1.35 0.17 6.09 1.35 0.17 6.09
5 563 70R 70R N CA 548 549 1.64 1.43 0.21 6.76 1.43 0.21 6.76
-------------------------------------------------------------------------------------------------
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 1702 49L 49L N CA 393 394 129.59 107.00 22.59 6.50 107.00 22.59 6.50
2 1713 50I 50I N CA 401 402 139.10 107.00 32.10 9.23 107.00 32.10 9.23
3 1717 50I 50I CA C 402 407 133.54 116.50 17.04 4.90 116.50 17.04 4.90
4 1903 69S 69S CA C 543 546 137.80 116.50 21.30 6.12 116.50 21.30 6.12
-------------------------------------------------------------------------------------------------
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 4562 3K 50I CA CA 19 402 12.02 9.92 2.10 4.66 9.92 2.10 4.66
2 5381 50I 56R CA CA 402 446 7.61 5.65 1.96 6.33 5.65 1.96 6.33
-------------------------------------------------------------------------------------------------
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 7284 50I 5R N O 401 45 12.49 9.64 2.85 5.10 9.64 2.85 5.10
2 7285 50I 8L N O 401 71 12.23 9.87 2.37 4.88 9.87 2.37 4.88
3 7291 50I 47V N O 401 386 5.50 3.33 2.17 6.01 3.33 2.17 6.01
4 7311 50I 135L N O 401 1090 12.83 9.76 3.07 5.54 9.76 3.07 5.54
-------------------------------------------------------------------------------------------------
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 4103 38F 38F CA C 296 304 -155.65 -180.00 24.35 4.87 -180.00 24.35 4.87
2 4134 69S 69S CA C 543 546 -134.78 -180.00 45.22 9.04 -180.00 45.22 9.04
-------------------------------------------------------------------------------------------------
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 3935 9L 10A C N 78 80 -169.92 -134.00 36.23 1.03 -62.50 -161.11 38.30
1 10A 10A N CA 80 81 151.71 147.00 -40.90
2 3936 10A 11L C N 83 85 -92.42 -108.50 16.10 0.76 -63.50 175.33 22.85
2 11L 11L N CA 85 86 131.73 132.50 -41.20
3 3937 11L 12A C N 91 93 -120.96 -134.00 20.74 0.71 -62.50 -178.56 27.53
3 12A 12A N CA 93 94 130.87 147.00 -40.90
4 3938 12A 13A C N 96 98 164.40 -134.00 85.05 2.49 -62.50 174.91 35.24
4 13A 13A N CA 98 99 -154.37 147.00 -40.90
5 3939 13A 14L C N 101 103 -59.43 -70.70 12.57 0.93 -63.50 177.28 24.85
5 14L 14L N CA 103 104 136.03 141.60 -41.20
6 3942 16I 17S C N 123 125 -149.43 -136.60 13.67 0.44 -64.10 -170.61 19.84
6 17S 17S N CA 125 126 155.92 151.20 -35.00
7 3943 17S 18C C N 129 131 -64.45 -63.00 4.10 0.61 -117.90 -178.01 7.83
7 18C 18C N CA 131 132 -44.93 -41.10 141.10
8 3944 18C 19E C N 135 137 -132.82 -117.80 17.42 0.51 -63.60 -172.66 28.88
8 19E 19E N CA 137 138 145.61 136.80 -40.30
9 3945 19E 20A C N 144 146 -83.50 -68.20 21.68 1.37 -62.50 159.82 27.27
9 20A 20A N CA 146 147 160.67 145.30 -40.90
10 3946 20A 21K C N 149 151 61.80 56.60 11.88 0.60 -62.90 142.38 24.87
10 21K 21K N CA 151 152 27.92 38.60 -40.80
11 3947 21K 22Y C N 158 160 -111.51 -98.40 13.92 0.67 -63.50 173.88 25.32
11 22Y 22Y N CA 160 161 123.72 128.40 -43.40
12 3948 22Y 23F C N 170 172 -75.14 -71.40 7.13 0.63 -63.20 179.33 24.11
12 23F 23F N CA 172 173 134.63 140.70 -44.30
13 3949 23F 24A C N 181 183 -157.65 -134.00 27.84 0.66 -62.50 -176.07 35.21
13 24A 24A N CA 183 184 161.69 147.00 -40.90
14 3951 25T 26N C N 193 195 56.33 55.90 16.71 1.14 -63.20 135.53 22.27
14 26N 26N N CA 195 196 22.80 39.50 -41.10
15 3953 27C 28E C N 207 209 -67.28 -63.60 49.94 6.86 -63.60 49.94 6.86
15 28E 28E N CA 209 210 -90.11 -40.30 -40.30
16 3956 30V 31H C N 231 233 -176.94 -125.60 67.89 3.06 -63.20 177.81 19.41
16 31H 31H N CA 233 234 94.37 138.80 -42.30
17 3974 48C 49L C N 391 393 -80.98 -63.50 48.09 7.76 -63.50 48.09 7.76
17 49L 49L N CA 393 394 -86.00 -41.20 -41.20
18 3975 49L 50I C N 399 401 -7.24 -63.40 56.97 9.84 -63.40 56.97 9.84
18 50I 50I N CA 401 402 -53.23 -43.60 -43.60
19 3989 63T 64I C N 503 505 -56.73 -63.40 14.19 2.16 -120.60 -175.05 12.94
19 64I 64I N CA 505 506 -56.13 -43.60 130.30
20 4011 85K 86T C N 689 691 73.71 55.90 45.36 2.19 -124.80 -142.48 13.12
20 86T 86T N CA 691 692 -2.22 39.50 143.50
21 4017 91K 92D C N 729 731 -134.58 -63.30 81.68 13.95 -63.30 81.68 13.95
21 92D 92D N CA 731 732 -79.88 -40.00 -40.00
22 4041 115I 116Y C N 906 908 -46.86 -98.40 52.81 2.46 -63.50 161.15 26.43
22 116Y 116Y N CA 908 909 116.89 128.40 -43.40
23 4055 129N 130H C N 1045 1047 -133.03 -63.20 82.82 10.27 -63.20 82.82 10.27
23 130H 130H N CA 1047 1048 2.23 -42.30 -42.30
24 4058 132Q 133G C N 1070 1072 128.57 78.70 55.02 2.01 82.20 168.66 10.42
24 133G 133G N CA 1072 1073 170.66 -166.10 8.50
25 4059 133G 134T C N 1074 1076 -105.74 -124.80 41.32 1.31 -63.20 154.89 17.40
25 134T 134T N CA 1076 1077 106.83 143.50 -42.10
26 4062 136P 137D C N 1096 1098 -53.95 -70.90 18.01 1.11 -63.30 176.04 21.18
26 137D 137D N CA 1098 1099 144.21 150.30 -40.00
27 4063 137D 138I C N 1104 1106 51.37 -97.30 160.69 8.31 -120.60 -178.55 14.07
27 138I 138I N CA 1106 1107 -171.82 127.20 130.30
28 4064 138I 139S C N 1112 1114 82.06 56.90 61.14 2.50 -64.10 147.00 19.30
28 139S 139S N CA 1114 1115 -19.32 36.40 -35.00
29 4065 139S 140K C N 1118 1120 37.07 56.60 30.05 1.77 -62.90 143.00 24.28
29 140K 140K N CA 1120 1121 61.44 38.60 -40.80
-------------------------------------------------------------------------------------------------
Feature 27 : Distance restraints 5 (X-Y)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 11694 142. 142. O4 O6 1146 1148 3.69 3.43 0.26 5.13 3.43 0.26 5.13
2 11719 142. 142. O6 O4 1148 1146 3.69 3.43 0.26 5.13 3.43 0.26 5.13
3 12127 50I 142. N O6 401 1148 10.36 3.00 7.36 73.58 3.00 7.36 73.58
4 12128 70R 144. N O6 548 1175 8.17 3.00 5.17 51.70 3.00 5.17 51.70
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 1 21 28 93 98 156 160 151 200 196 195
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
TRINI_L.B99990001.pdb 5646.90918
TRINI_L.B99990002.pdb 5820.80908
In [82]:
cmd.load('TRINI_L.B99990001.pdb', 'model1')
cmd.load('1lmp.pdb', 'source')
cmd.do('align model1, source')
cmd.bg_color('white')
cmd.set('ray_trace_mode', 3)
In [83]:
cmd.do('ray; png 2+l.png')
In [84]:
display(Image('2+2.png'), Image('2+l.png'))
Лиганд немного поменял свое положение. Этакий докинг на минималках, только без вменяемой точности.
Теперь сделаем "Лизоцим" целиком из аланинов. Я априорно слабо понимаю смысл этой манипуляции, кроме того, чтобы понять, насколько modeller подгоняет данные. Очевидно, что в реальности лизоцим из аланинов не сложится...
In [85]:
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')
seq_ala = 'A' * 129 + '...'
alignm.append_sequence(seq_ala)
alignm[0].code = 'pdb'
alignm[1].code = 'seq_ala'
In [86]:
alignm.salign()
alignm.write(file='all_in_one_ala.ali', alignment_format='PIR')
In [87]:
! cat all_in_one_ala.ali
???
In [88]:
## 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_one_ala.ali', knowns=pdb.code, sequence=s.code)
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
In [89]:
cmd.reinitialize()
In [90]:
cmd.load('seq_ala.B99990001.pdb', 'model1')
cmd.load('1lmp.pdb', 'source')
cmd.do('align model1, source')
cmd.bg_color('white')
cmd.set('ray_trace_mode', 3)
In [94]:
cmd.do('ray; png ala.png')
In [95]:
Image('ala.png')
Out[95]:
Какая хорошая, а главное, правдоподобная структура. Кто бы мог подумать, что из полиаланина свернется лизоцим? Я вот не мог.
\</sarcasm> На самом деле, это говорит о том, что предназначение этого метода не построение структуры булка, а создание базового каркаса для какого-нибудь более мощного метода. Что мы, в общем-то уже и так понимали.