Домашнее задание №6¶
Запускаем modeller:
In [43]:
import sys
import modeller
import _modeller
import modeller.automodel
import nglview
import ipywidgets
from IPython.display import Image
In [44]:
env=modeller.environ()
env.io.hetatm=True
In [45]:
!wget -O - 'http://www.pdb.org/pdb/files/1lmp.pdb' > 1lmp.pdb
--2017-12-08 12:22:50-- 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]
--2017-12-08 12:22:51-- https://www.rcsb.org/pdb/files/1lmp.pdb
Resolving www.rcsb.org (www.rcsb.org)... 132.249.213.110
Connecting to www.rcsb.org (www.rcsb.org)|132.249.213.110|:443... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: http://files.rcsb.org/view/1lmp.pdb [following]
--2017-12-08 12:22:52-- http://files.rcsb.org/view/1lmp.pdb
Resolving files.rcsb.org (files.rcsb.org)... 132.249.213.140
Connecting to files.rcsb.org (files.rcsb.org)|132.249.213.140|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [text/plain]
Saving to: `STDOUT'
[ <=> ] 131,301 154K/s in 0.8s
2017-12-08 12:22:53 (154 KB/s) - written to stdout [131301]
Зааплодим белок Lysozyme C-2(Mouse)
In [46]:
!wget -O - 'http://www.uniprot.org/uniprot/P08905.fasta' > P08905.fasta
--2017-12-08 12:22:59-- http://www.uniprot.org/uniprot/P08905.fasta Resolving www.uniprot.org (www.uniprot.org)... 193.62.193.81, 128.175.240.211 Connecting to www.uniprot.org (www.uniprot.org)|193.62.193.81|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 220 [text/plain] Saving to: `STDOUT' 100%[======================================>] 220 --.-K/s in 0s 2017-12-08 12:22:59 (28.1 MB/s) - written to stdout [220/220]
In [47]:
alignm=modeller.alignment(env)
In [48]:
alignm.append(file='P08905.fasta', align_codes='all',alignment_format='FASTA')
## создадим модель
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
## и добавим в выравнивание
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
## есть смысл поправить идентификаторы
alignm[0].code = 'P08905'
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 [50]:
#align and save
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [51]:
## Выбираем объект для моделирования
s= alignm[0]
pdb = alignm[1]
print s.code, pdb.code
P08905 1lmp
In [52]:
## 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 = 1
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
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: 13318 12311
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 : 148
Number of all, selected real atoms : 1169 1169
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12311 12311
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2329
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 : 793.5898
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 : 1190 0 0 0.006 0.006 11.854 1.000
2 Bond angle potential : 1613 0 6 2.069 2.069 139.00 1.000
3 Stereochemical cosine torsion poten: 757 0 32 48.388 48.388 277.79 1.000
4 Stereochemical improper torsion pot: 504 0 0 1.339 1.339 20.410 1.000
5 Soft-sphere overlap restraints : 2329 0 0 0.001 0.001 0.53073 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 0 0.123 0.123 36.292 1.000
10 Distance restraints 2 (N-O) : 2564 0 0 0.148 0.148 63.415 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: 147 0 2 4.204 4.204 30.641 1.000
14 Sidechain Chi_1 dihedral restraints: 122 0 1 59.052 59.052 16.799 1.000
15 Sidechain Chi_2 dihedral restraints: 89 0 0 65.220 65.220 35.103 1.000
16 Sidechain Chi_3 dihedral restraints: 34 0 0 84.757 84.757 25.975 1.000
17 Sidechain Chi_4 dihedral restraints: 18 0 0 91.823 91.823 11.364 1.000
18 Disulfide distance restraints : 4 0 0 0.015 0.015 0.15684 1.000
19 Disulfide angle restraints : 8 0 0 2.096 2.096 0.77587 1.000
20 Disulfide dihedral angle restraints: 4 0 0 24.138 24.138 2.2724 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) : 1742 0 0 0.391 0.391 38.970 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: 146 16 12 21.216 59.735 27.869 1.000
26 Distance restraints 4 (SDCH-SDCH) : 964 0 1 0.625 0.625 54.367 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: P08905.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: 14374.0479
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 4081 1M 2K C N 7 9 -118.73 -118.00 18.65 0.90 -62.90 170.84 25.52
1 2K 2K N CA 9 10 157.74 139.10 -40.80
2 4082 2K 3T C N 16 18 -114.68 -124.80 32.25 1.67 -63.20 152.72 22.99
2 3T 3T N CA 18 19 174.12 143.50 -42.10
3 4083 3T 4L C N 23 25 -101.28 -108.50 34.88 1.80 -63.50 144.60 18.28
3 4L 4L N CA 25 26 98.37 132.50 -41.20
4 4084 4L 5L C N 31 33 -169.88 -108.50 92.58 4.22 -63.50 158.13 28.25
4 5L 5L N CA 33 34 -158.20 132.50 -41.20
5 4085 5L 6T C N 39 41 -57.48 -78.10 21.81 1.11 -63.20 175.31 22.11
5 6T 6T N CA 41 42 142.68 149.80 -42.10
6 4086 6T 7L C N 46 48 -85.80 -70.70 24.71 1.54 -63.50 159.21 23.45
6 7L 7L N CA 48 49 161.15 141.60 -41.20
7 4088 8G 9L C N 58 60 -70.12 -70.70 20.60 1.58 -63.50 156.74 22.15
7 9L 9L N CA 60 61 162.20 141.60 -41.20
8 4090 10L 11L C N 74 76 -58.92 -70.70 12.23 0.99 -63.50 179.56 25.20
8 11L 11L N CA 76 77 138.30 141.60 -41.20
9 4092 12L 13S C N 90 92 -110.41 -136.60 40.78 1.38 -64.10 161.71 9.98
9 13S 13S N CA 92 93 119.93 151.20 -35.00
10 4094 14V 15T C N 103 105 -136.56 -124.80 20.26 0.63 -63.20 174.10 27.12
10 15T 15T N CA 105 106 160.00 143.50 -42.10
11 4095 15T 16A C N 110 112 -99.18 -68.20 42.61 4.20 -62.50 161.19 24.88
11 16A 16A N CA 112 113 116.06 145.30 -40.90
12 4096 16A 17Q C N 115 117 -86.84 -73.00 17.00 1.33 -63.80 172.69 24.24
12 17Q 17Q N CA 117 118 130.84 140.70 -40.30
13 4097 17Q 18A C N 124 126 -116.31 -134.00 21.09 0.51 -62.50 -175.57 28.12
13 18A 18A N CA 126 127 135.51 147.00 -40.90
14 4098 18A 19K C N 129 131 -136.42 -118.00 18.61 0.75 -62.90 -168.13 22.14
14 19K 19K N CA 131 132 136.42 139.10 -40.80
15 4133 53E 54S C N 413 415 -137.79 -64.10 84.10 8.50 -64.10 84.10 8.50
15 54S 54S N CA 415 416 5.53 -35.00 -35.00
16 4145 65R 66G C N 516 518 -64.36 -62.40 10.44 1.66 82.20 158.36 12.18
16 66G 66G N CA 518 519 -51.45 -41.20 8.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 4 12 41 65 100 114 137 153 172 169
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
P08905.B99990001.pdb 793.58984
In [53]:
w1 = nglview.show_structure_file('P08905.B99990001.pdb')
w1
Как видно на картинке снизу - при создании гомологичного белка не отобразился лиганд.
In [56]:
Image("P08905.png")
Out[56]:
In [57]:
## Получить список остаков
res=alignm[1].residues
## Добавить в объект выравнивание последовательность из строки
#alignm.append_sequence(....
res
Out[57]:
132 residues
In [58]:
for i in range(1,len(res)):
print res[i]
print (len(res))
<Residue 2:A (type VAL)> <Residue 3:A (type TYR)> <Residue 4:A (type ASP)> <Residue 5:A (type ARG)> <Residue 6:A (type CYS)> <Residue 7:A (type GLU)> <Residue 8:A (type LEU)> <Residue 9:A (type ALA)> <Residue 10:A (type ARG)> <Residue 11:A (type ALA)> <Residue 12:A (type LEU)> <Residue 13:A (type LYS)> <Residue 14:A (type ALA)> <Residue 15:A (type SER)> <Residue 16:A (type GLY)> <Residue 17:A (type MET)> <Residue 18:A (type ASP)> <Residue 19:A (type GLY)> <Residue 20:A (type TYR)> <Residue 21:A (type ALA)> <Residue 22:A (type GLY)> <Residue 23:A (type ASN)> <Residue 24:A (type SER)> <Residue 25:A (type LEU)> <Residue 26:A (type PRO)> <Residue 27:A (type ASN)> <Residue 28:A (type TRP)> <Residue 29:A (type VAL)> <Residue 30:A (type CYS)> <Residue 31:A (type LEU)> <Residue 32:A (type SER)> <Residue 33:A (type LYS)> <Residue 34:A (type TRP)> <Residue 35:A (type GLU)> <Residue 36:A (type SER)> <Residue 37:A (type SER)> <Residue 38:A (type TYR)> <Residue 39:A (type ASN)> <Residue 40:A (type THR)> <Residue 41:A (type GLN)> <Residue 42:A (type ALA)> <Residue 43:A (type THR)> <Residue 44:A (type ASN)> <Residue 45:A (type ARG)> <Residue 46:A (type ASN)> <Residue 47:A (type THR)> <Residue 48:A (type ASP)> <Residue 49:A (type GLY)> <Residue 50:A (type SER)> <Residue 51:A (type THR)> <Residue 52:A (type ASP)> <Residue 53:A (type TYR)> <Residue 54:A (type GLY)> <Residue 55:A (type ILE)> <Residue 56:A (type PHE)> <Residue 57:A (type GLN)> <Residue 58:A (type ILE)> <Residue 59:A (type ASN)> <Residue 60:A (type SER)> <Residue 61:A (type ARG)> <Residue 62:A (type TYR)> <Residue 63:A (type TRP)> <Residue 64:A (type CYS)> <Residue 65:A (type ASP)> <Residue 66:A (type ASP)> <Residue 67:A (type GLY)> <Residue 68:A (type ARG)> <Residue 69:A (type THR)> <Residue 70:A (type PRO)> <Residue 71:A (type GLY)> <Residue 72:A (type ALA)> <Residue 73:A (type LYS)> <Residue 74:A (type ASN)> <Residue 75:A (type VAL)> <Residue 76:A (type CYS)> <Residue 77:A (type GLY)> <Residue 78:A (type ILE)> <Residue 79:A (type ARG)> <Residue 80:A (type CYS)> <Residue 81:A (type SER)> <Residue 82:A (type GLN)> <Residue 83:A (type LEU)> <Residue 84:A (type LEU)> <Residue 85:A (type THR)> <Residue 86:A (type ASP)> <Residue 87:A (type ASP)> <Residue 88:A (type LEU)> <Residue 89:A (type THR)> <Residue 90:A (type VAL)> <Residue 91:A (type ALA)> <Residue 92:A (type ILE)> <Residue 93:A (type ARG)> <Residue 94:A (type CYS)> <Residue 95:A (type ALA)> <Residue 96:A (type LYS)> <Residue 97:A (type ARG)> <Residue 98:A (type VAL)> <Residue 99:A (type VAL)> <Residue 100:A (type LEU)> <Residue 101:A (type ASP)> <Residue 102:A (type PRO)> <Residue 103:A (type ASN)> <Residue 104:A (type GLY)> <Residue 105:A (type ILE)> <Residue 106:A (type GLY)> <Residue 107:A (type ALA)> <Residue 108:A (type TRP)> <Residue 109:A (type VAL)> <Residue 110:A (type ALA)> <Residue 111:A (type TRP)> <Residue 112:A (type ARG)> <Residue 113:A (type LEU)> <Residue 114:A (type HIS)> <Residue 115:A (type CYS)> <Residue 116:A (type GLN)> <Residue 117:A (type ASN)> <Residue 118:A (type GLN)> <Residue 119:A (type ASP)> <Residue 120:A (type LEU)> <Residue 121:A (type ARG)> <Residue 122:A (type SER)> <Residue 123:A (type TYR)> <Residue 124:A (type VAL)> <Residue 125:A (type ALA)> <Residue 126:A (type GLY)> <Residue 127:A (type CYS)> <Residue 128:A (type GLY)> <Residue 129:A (type VAL)> <Residue 130:A (type NAG)> <Residue 131:A (type NAG)> <Residue 132:A (type NDG)> 132
Как видно, последние три основания - это лиганд. Возьмем последовательность белка P08905 и прибавим три '.' , чтобы при выравнивании появился лиганд.
In [59]:
seq=''
for i in range(1,len(alignm[0].residues)):
seq=seq+alignm[0].residues[i].code
seq=seq+'...'
In [60]:
seq
Out[60]:
'KTLLTLGLLLLSVTAQAKVYERCEFARTLKRNGMAGYYGVSLADWVCLAQHESNYNTRATNYNRGDQSTDYGIFQINSRYWCNDGKTPRAVNACGINCSALLQDDITAAIQCAKRVVRDPQGIRAWVAWRAHCQNRDLSQYIRNCGV...'
In [61]:
alignm.append_sequence(seq)
In [62]:
res2=alignm[2].residues
for i in range(1,len(res2)):
print res2[i]
print (len(res2))
<Residue THR> <Residue LEU> <Residue LEU> <Residue THR> <Residue LEU> <Residue GLY> <Residue LEU> <Residue LEU> <Residue LEU> <Residue LEU> <Residue SER> <Residue VAL> <Residue THR> <Residue ALA> <Residue GLN> <Residue ALA> <Residue LYS> <Residue VAL> <Residue TYR> <Residue GLU> <Residue ARG> <Residue CYS> <Residue GLU> <Residue PHE> <Residue ALA> <Residue ARG> <Residue THR> <Residue LEU> <Residue LYS> <Residue ARG> <Residue ASN> <Residue GLY> <Residue MET> <Residue ALA> <Residue GLY> <Residue TYR> <Residue TYR> <Residue GLY> <Residue VAL> <Residue SER> <Residue LEU> <Residue ALA> <Residue ASP> <Residue TRP> <Residue VAL> <Residue CYS> <Residue LEU> <Residue ALA> <Residue GLN> <Residue HIS> <Residue GLU> <Residue SER> <Residue ASN> <Residue TYR> <Residue ASN> <Residue THR> <Residue ARG> <Residue ALA> <Residue THR> <Residue ASN> <Residue TYR> <Residue ASN> <Residue ARG> <Residue GLY> <Residue ASP> <Residue GLN> <Residue SER> <Residue THR> <Residue ASP> <Residue TYR> <Residue GLY> <Residue ILE> <Residue PHE> <Residue GLN> <Residue ILE> <Residue ASN> <Residue SER> <Residue ARG> <Residue TYR> <Residue TRP> <Residue CYS> <Residue ASN> <Residue ASP> <Residue GLY> <Residue LYS> <Residue THR> <Residue PRO> <Residue ARG> <Residue ALA> <Residue VAL> <Residue ASN> <Residue ALA> <Residue CYS> <Residue GLY> <Residue ILE> <Residue ASN> <Residue CYS> <Residue SER> <Residue ALA> <Residue LEU> <Residue LEU> <Residue GLN> <Residue ASP> <Residue ASP> <Residue ILE> <Residue THR> <Residue ALA> <Residue ALA> <Residue ILE> <Residue GLN> <Residue CYS> <Residue ALA> <Residue LYS> <Residue ARG> <Residue VAL> <Residue VAL> <Residue ARG> <Residue ASP> <Residue PRO> <Residue GLN> <Residue GLY> <Residue ILE> <Residue ARG> <Residue ALA> <Residue TRP> <Residue VAL> <Residue ALA> <Residue TRP> <Residue ARG> <Residue ALA> <Residue HIS> <Residue CYS> <Residue GLN> <Residue ASN> <Residue ARG> <Residue ASP> <Residue LEU> <Residue SER> <Residue GLN> <Residue TYR> <Residue ILE> <Residue ARG> <Residue ASN> <Residue CYS> <Residue GLY> <Residue VAL> <Residue BLK> <Residue BLK> <Residue BLK> 150
In [65]:
## есть смысл поправить идентификаторы
alignm[2].code = 'P08905_with_ligand'
## Выбираем объект для моделирования
s= alignm[2]
pdb = alignm[1]
print s.code, pdb.code
P08905_with_ligand 1lmp
In [66]:
alignm.salign()
alignm.write(file='all_in_one_new.ali', alignment_format='PIR')
## Создаем объект automodel
a_new = modeller.automodel.automodel(env, alnfile='all_in_one_new.ali', knowns= pdb.code , sequence = s.code )
a_new.name='mod'+s.code
a_new.starting_model = 1
a_new.ending_model = 1
a_new.make()
SALIGN_____> adding the next group to the alignment; iteration 1
SALIGN_____> adding the next group to the alignment; iteration 2
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: 18 147
atom names : C +N
atom indices : 1159 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 18 147
atom names : C CA +N O
atom indices : 1159 1155 0 1160
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 4
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/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: 14682 13684
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 : 1204 1204
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13684 13684
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2537
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 : 877.3222
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 : 1182 0 0 0.006 0.006 12.334 1.000
2 Bond angle potential : 1603 0 7 2.106 2.106 144.11 1.000
3 Stereochemical cosine torsion poten: 754 0 29 47.933 47.933 271.73 1.000
4 Stereochemical improper torsion pot: 502 0 0 1.296 1.296 19.484 1.000
5 Soft-sphere overlap restraints : 2537 2 2 0.007 0.007 16.764 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 0 0.118 0.118 35.148 1.000
10 Distance restraints 2 (N-O) : 2564 0 0 0.149 0.149 63.988 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 3 4.594 4.594 36.337 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 1 69.775 69.775 21.950 1.000
15 Sidechain Chi_2 dihedral restraints: 88 0 0 63.981 63.981 35.356 1.000
16 Sidechain Chi_3 dihedral restraints: 33 0 0 86.630 86.630 21.218 1.000
17 Sidechain Chi_4 dihedral restraints: 18 0 0 109.015 109.015 9.5670 1.000
18 Disulfide distance restraints : 4 0 0 0.008 0.008 0.43430E-01 1.000
19 Disulfide angle restraints : 8 0 0 1.842 1.842 0.59932 1.000
20 Disulfide dihedral angle restraints: 4 0 0 31.044 31.044 3.4944 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) : 1742 0 0 0.475 0.475 59.340 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 16 19.486 58.889 22.077 1.000
26 Distance restraints 4 (SDCH-SDCH) : 964 0 0 0.778 0.778 87.660 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.036 0.036 16.122 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: P08905_with_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: 15786.7471
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 4058 1K 2T C N 8 10 -130.61 -124.80 14.91 0.49 -63.20 174.24 26.78
1 2T 2T N CA 10 11 157.23 143.50 -42.10
2 4059 2T 3L C N 15 17 -77.00 -70.70 6.68 0.66 -63.50 179.90 25.77
2 3L 3L N CA 17 18 139.41 141.60 -41.20
3 4060 3L 4L C N 23 25 -73.61 -70.70 15.40 1.06 -63.50 162.39 23.14
3 4L 4L N CA 25 26 156.72 141.60 -41.20
4 4061 4L 5T C N 31 33 -76.04 -78.10 44.64 1.98 -63.20 124.17 16.78
4 5T 5T N CA 33 34 -165.61 149.80 -42.10
5 4062 5T 6L C N 38 40 -62.69 -70.70 12.29 1.21 -63.50 167.87 23.26
5 6L 6L N CA 40 41 150.93 141.60 -41.20
6 4064 7G 8L C N 50 52 -103.97 -108.50 11.84 0.58 -63.50 167.72 21.33
6 8L 8L N CA 52 53 121.56 132.50 -41.20
7 4065 8L 9L C N 58 60 -107.63 -108.50 8.25 0.44 -63.50 171.28 21.68
7 9L 9L N CA 60 61 124.30 132.50 -41.20
8 4066 9L 10L C N 66 68 -124.04 -108.50 18.34 0.81 -63.50 -173.34 29.66
8 10L 10L N CA 68 69 142.23 132.50 -41.20
9 4067 10L 11L C N 74 76 -82.36 -108.50 49.08 2.32 -63.50 133.50 17.54
9 11L 11L N CA 76 77 90.96 132.50 -41.20
10 4068 11L 12S C N 82 84 -91.94 -72.40 26.24 1.27 -64.10 157.57 13.27
10 12S 12S N CA 84 85 169.91 152.40 -35.00
11 4069 12S 13V C N 88 90 -64.92 -62.40 3.86 0.64 -125.40 -178.27 10.17
11 13V 13V N CA 90 91 -45.32 -42.40 143.30
12 4071 14T 15A C N 102 104 -130.23 -134.00 4.67 0.26 -62.50 -177.61 33.52
12 15A 15A N CA 104 105 149.75 147.00 -40.90
13 4072 15A 16Q C N 107 109 -139.99 -121.10 36.28 1.33 -63.80 167.37 28.57
13 16Q 16Q N CA 109 110 170.67 139.70 -40.30
14 4073 16Q 17A C N 116 118 -61.07 -68.20 8.70 0.86 -62.50 168.81 27.60
14 17A 17A N CA 118 119 150.30 145.30 -40.90
15 4074 17A 18K C N 121 123 -106.44 -118.00 15.17 0.52 -62.90 175.56 20.83
15 18K 18K N CA 123 124 129.27 139.10 -40.80
16 4109 52E 53S C N 405 407 -138.24 -64.10 82.09 8.63 -64.10 82.09 8.63
16 53S 53S N CA 407 408 0.25 -35.00 -35.00
17 4121 64R 65G C N 508 510 -68.60 -62.40 6.27 1.08 82.20 158.49 12.00
17 65G 65G N CA 510 511 -40.26 -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 8 45 92 113 128 146 163 185 212
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
P08905_with_ligand.B99990001.pdb 877.32220
In [67]:
new_protein = nglview.show_structure_file('P08905_with_ligand.B99990001.pdb')
new_protein
При сохранении html -страницы картинка теряется, поэтому сохраню и загружу через ИМАГЕ
In [68]:
Image("P08905_new.png")
Out[68]:
In [ ]: