! cd /tmp/ ; wget https://salilab.org/modeller/10.1/modeller_10.1-1_amd64.deb
! env KEY_MODELLER="MODELIRANJE" dpkg -i /tmp/modeller_10.1-1_amd64.deb
--2023-05-10 10:11:34-- https://salilab.org/modeller/10.1/modeller_10.1-1_amd64.deb Resolving salilab.org (salilab.org)... 169.230.79.19 Connecting to salilab.org (salilab.org)|169.230.79.19|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 14404568 (14M) [application/vnd.debian.binary-package] Saving to: ‘modeller_10.1-1_amd64.deb’ modeller_10.1-1_amd 100%[===================>] 13.74M 14.1MB/s in 1.0s 2023-05-10 10:11:35 (14.1 MB/s) - ‘modeller_10.1-1_amd64.deb’ saved [14404568/14404568] Selecting previously unselected package modeller. (Reading database ... 122518 files and directories currently installed.) Preparing to unpack /tmp/modeller_10.1-1_amd64.deb ... Unpacking modeller (10.1-1) ... Setting up modeller (10.1-1) ...
import os
os.kill(os.getpid(), 9)
! echo -e "install_dir = r'/usr/lib/modeller10.1'\nlicense = 'MODELIRANJE'" > /usr/lib/modeller10.1/modlib/modeller/config.py
! pip install nglview
import nglview
from google.colab import output
output.enable_custom_widget_manager()
Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/
Collecting nglview
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Collecting jedi>=0.16 (from ipython>=4.0.0->ipywidgets>=7->nglview)
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))': /packages/6d/60/4acda63286ef6023515eb914543ba36496b8929cb7af49ecce63afde09c6/jedi-0.18.2-py2.py3-none-any.whl
Downloading jedi-0.18.2-py2.py3-none-any.whl (1.6 MB)
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Building wheels for collected packages: nglview
Building wheel for nglview (pyproject.toml) ... done
Created wheel for nglview: filename=nglview-3.0.4-py3-none-any.whl size=11032140 sha256=3789d5e5672107f86b774954c6aee4ab6080596c19c7f7b76607ccb86550903f
Stored in directory: /root/.cache/pip/wheels/a2/4b/b3/665a9eb517518b7c2341df9b77f40584e8844d3a8eb3ccba1b
Successfully built nglview
Installing collected packages: jedi, nglview
Successfully installed jedi-0.18.2 nglview-3.0.4
import sys
sys.path.append('/usr/lib/python3.9/dist-packages')
import modeller
import _modeller
import modeller.automodel
import numpy as np
from IPython.display import display,Image
env=modeller.Environ()
env.io.hetatm=True
MODELLER 10.1, 2021/03/12, r12156
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2021 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux 5769a21f2787 5.10.147+ x86_64
Date and time of compilation : 2021/03/12 00:18:43
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2023/05/10 10:12:38
! wget -q -O template.pdb http://www.pdb.org/pdb/files/1lmp.pdb
! wget -q -O sequence.fasta http://www.uniprot.org/uniprot/P03706.fasta
env=modeller.environ()
env.io.hetatm=True
alignm=modeller.alignment(env)
environ____W> The class 'environ' is deprecated; use 'Environ' instead alignment__W> The class 'alignment' is deprecated; use 'Alignment' instead
alignm.append(file='sequence.fasta', align_codes='all',alignment_format='FASTA')
mdl = modeller.model(env, file='template.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
alignm.append_model(mdl, atom_files='template.pdb', align_codes='template')
alignm[0].code = 'LYS_LAMBD'
alignm[1].code = '1lmp'
model______W> The class 'model' is deprecated; use 'Model' instead
alignm.salign()
alignm.write(file='a.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
! cat a.ali
>P1;LYS_LAMBD sequence::: :: :::-1.00:-1.00 MVEINNQRKAFLDMLAWSEGTDNGRQKTRNHGYDVIVGGELFTDYSDHPRKLVTLNPKLKSTGAGRYQLLSRWWD AYRKQLGLKDFSPKSQDAVALQQIKERGALPMIDRGDIRQAIDRCSNIWASLPGAGYGQFEHKADSLIAKFKEAG GTVREIDV* >P1;1lmp structureX:template.pdb:1:A:+129: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 KVYDRCELARALKASGMDGYAGNS-----------LPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWC DDGRTPGAKNVCGIRCSQLL--------------TDDLTVAIRCAKRVVLDPNGIG----AWVAWRLHCQNQDLR SYVAGCGV*
Нет лиганда. Давайте добавим...
with open('a.ali','r') as old:
lines = old.readlines()
with open('a_lig.ali','w') as new:
for c, line in enumerate(lines):
if c == 5:
line = line[:-2] + '/...*\n'
if c == 11:
line = line[:-2] + '/...*'
new.write(line)
! sed -i 's/129/132/g' a_lig.ali
! cat a_lig.ali
>P1;LYS_LAMBD sequence::: :: :::-1.00:-1.00 MVEINNQRKAFLDMLAWSEGTDNGRQKTRNHGYDVIVGGELFTDYSDHPRKLVTLNPKLKSTGAGRYQLLSRWWD AYRKQLGLKDFSPKSQDAVALQQIKERGALPMIDRGDIRQAIDRCSNIWASLPGAGYGQFEHKADSLIAKFKEAG GTVREIDV/...* >P1;1lmp structureX:template.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 KVYDRCELARALKASGMDGYAGNS-----------LPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWC DDGRTPGAKNVCGIRCSQLL--------------TDDLTVAIRCAKRVVLDPNGIG----AWVAWRLHCQNQDLR SYVAGCGV/...*
s = alignm[0]
pdb = alignm[1]
a = modeller.automodel.automodel(env, alnfile='a_lig.ali', knowns= pdb.code , sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 1
a.make()
automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead
read_pd_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.
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.
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.)
The following 1 residues contain 6-membered rings with poor geometries
after transfer from templates. Rebuilding rings from internal coordinates:
<Residue 45:A (type TYR)>
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
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: 13524 12408
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
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 : 161
Number of all, selected real atoms : 1300 1300
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12408 12408
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3574
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 : 1328.0875
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 : 1282 0 0 0.006 0.006 12.750 1.000
2 Bond angle potential : 1726 0 6 2.267 2.267 174.18 1.000
3 Stereochemical cosine torsion poten: 789 0 42 50.119 50.119 308.92 1.000
4 Stereochemical improper torsion pot: 515 0 0 1.417 1.417 21.411 1.000
5 Soft-sphere overlap restraints : 3574 2 2 0.008 0.008 26.411 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) : 2407 0 1 0.448 0.448 116.32 1.000
10 Distance restraints 2 (N-O) : 2568 1 25 0.586 0.586 252.19 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: 157 0 10 5.751 5.751 61.232 1.000
14 Sidechain Chi_1 dihedral restraints: 130 0 4 86.830 86.830 63.581 1.000
15 Sidechain Chi_2 dihedral restraints: 107 0 0 74.297 74.297 48.240 1.000
16 Sidechain Chi_3 dihedral restraints: 48 0 0 77.003 77.003 31.653 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 97.908 97.908 16.316 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 941 0 0 0.482 0.482 21.161 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: 156 47 32 37.875 93.666 142.85 1.000
26 Distance restraints 4 (SDCH-SDCH) : 157 0 1 1.100 1.100 17.796 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.032 0.032 13.087 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: LYS_LAMBD.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: 23339.5781
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 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 7774 36I 17W N O 287 144 7.70 4.62 3.08 4.94 4.62 3.08 4.94
-------------------------------------------------------------------------------------------------
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 4327 15L 16A C N 124 126 78.83 55.40 28.81 1.90 -62.50 154.46 31.36
1 16A 16A N CA 126 127 21.44 38.20 -40.90
2 4330 18S 19E C N 149 151 62.38 54.60 20.24 1.06 -63.60 141.31 24.27
2 19E 19E N CA 151 152 23.71 42.40 -40.30
3 4332 20G 21T C N 162 164 47.19 55.90 10.32 0.78 -124.80 -161.83 7.58
3 21T 21T N CA 164 165 45.04 39.50 143.50
4 4335 23N 24G C N 185 187 -75.15 -80.20 42.24 1.41 82.20 -159.87 7.22
4 24G 24G N CA 187 188 132.17 174.10 8.50
5 4336 24G 25R C N 189 191 -115.03 -125.20 29.21 1.16 -63.00 162.85 19.10
5 25R 25R N CA 191 192 113.21 140.60 -41.10
6 4337 25R 26Q C N 200 202 -110.47 -121.10 36.86 1.55 -63.80 152.05 20.23
6 26Q 26Q N CA 202 203 104.40 139.70 -40.30
7 4338 26Q 27K C N 209 211 -179.80 -118.00 69.95 2.32 -62.90 -171.93 31.26
7 27K 27K N CA 211 212 171.87 139.10 -40.80
8 4339 27K 28T C N 218 220 -137.68 -124.80 89.88 3.48 -63.20 113.35 19.03
8 28T 28T N CA 220 221 -127.55 143.50 -42.10
9 4340 28T 29R C N 225 227 -128.20 -125.20 21.09 1.08 -63.00 173.53 20.01
9 29R 29R N CA 227 228 119.72 140.60 -41.10
10 4341 29R 30N C N 236 238 -157.40 -119.90 49.67 1.44 -63.20 176.56 27.28
10 30N 30N N CA 238 239 169.57 137.00 -41.10
11 4342 30N 31H C N 244 246 -83.23 -67.60 21.18 1.25 -63.20 164.63 21.87
11 31H 31H N CA 246 247 154.29 140.00 -42.30
12 4344 32G 33Y C N 258 260 -108.12 -98.40 18.42 1.66 -63.50 162.40 23.66
12 33Y 33Y N CA 260 261 112.75 128.40 -43.40
13 4345 33Y 34D C N 270 272 -131.52 -70.90 63.16 4.07 -63.30 166.59 24.97
13 34D 34D N CA 272 273 168.02 150.30 -40.00
14 4347 35V 36I C N 285 287 -100.08 -120.60 24.48 1.18 -63.40 164.70 25.84
14 36I 36I N CA 287 288 116.96 130.30 -43.60
15 4358 46S 47D C N 369 371 -153.66 -96.50 92.12 3.79 -63.30 121.99 14.06
15 47D 47D N CA 371 372 41.96 114.20 -40.00
16 4359 47D 48H C N 377 379 63.37 -67.60 137.54 11.51 56.30 141.38 13.11
16 48H 48H N CA 379 380 -178.00 140.00 40.80
17 4360 48H 49P C N 387 389 -79.66 -58.70 50.42 2.96 -64.50 132.71 10.72
17 49P 49P N CA 389 390 15.36 -30.50 147.20
18 4379 67Y 68Q C N 534 536 62.14 55.10 13.77 1.57 -121.10 -162.74 9.26
18 68Q 68Q N CA 536 537 52.14 40.30 139.70
19 4388 76A 77Y C N 617 619 -120.63 -63.50 90.14 12.44 -63.50 90.14 12.44
19 77Y 77Y N CA 619 620 26.32 -43.40 -43.40
20 4390 78R 79K C N 640 642 -147.89 -118.00 94.73 4.88 -62.90 123.80 14.91
20 79K 79K N CA 642 643 49.21 139.10 -40.80
21 4395 83L 84K C N 678 680 -134.32 -118.00 76.80 3.90 -62.90 126.87 14.71
21 84K 84K N CA 680 681 64.06 139.10 -40.80
22 4396 84K 85D C N 687 689 -41.70 -96.50 61.13 2.53 54.50 106.72 9.34
22 85D 85D N CA 689 690 87.11 114.20 40.90
23 4398 86F 87S C N 706 708 -101.87 -72.40 87.60 6.15 -64.10 111.50 6.87
23 87S 87S N CA 708 709 69.91 152.40 -35.00
24 4407 95A 96L C N 768 770 -150.70 -108.50 53.48 2.37 -63.50 176.50 29.88
24 96L 96L N CA 770 771 165.34 132.50 -41.20
25 4408 96L 97Q C N 776 778 -130.86 -121.10 17.03 0.60 -63.80 179.07 29.87
25 97Q 97Q N CA 778 779 153.66 139.70 -40.30
26 4409 97Q 98Q C N 785 787 62.67 -73.00 142.72 10.88 -63.80 -175.24 23.97
26 98Q 98Q N CA 787 788 -174.99 140.70 -40.30
27 4411 99I 100K C N 802 804 -62.44 -70.20 12.08 0.72 -62.90 171.95 22.35
27 100K 100K N CA 804 805 131.15 140.40 -40.80
28 4412 100K 101E C N 811 813 -145.73 -117.80 34.50 1.03 -63.60 -177.79 28.87
28 101E 101E N CA 813 814 157.05 136.80 -40.30
29 4413 101E 102R C N 820 822 -70.18 -72.10 3.68 0.32 -63.00 174.01 23.99
29 102R 102R N CA 822 823 145.04 141.90 -41.10
30 4414 102R 103G C N 831 833 -173.41 -167.20 12.06 0.35 82.20 -155.00 14.59
30 103G 103G N CA 833 834 -175.06 174.60 8.50
31 4415 103G 104A C N 835 837 -75.06 -68.20 17.36 1.17 -62.50 158.35 26.58
31 104A 104A N CA 837 838 161.25 145.30 -40.90
32 4416 104A 105L C N 840 842 93.22 -108.50 159.51 7.38 -63.50 -131.34 29.17
32 105L 105L N CA 842 843 152.30 132.50 -41.20
33 4417 105L 106P C N 848 850 -62.23 -58.70 5.74 0.75 -64.50 177.79 13.39
33 106P 106P N CA 850 851 -35.03 -30.50 147.20
34 4418 106P 107M C N 855 857 168.13 -125.60 72.60 2.23 -63.40 -163.00 38.84
34 107M 107M N CA 857 858 170.15 140.50 -40.50
35 4420 108I 109D C N 871 873 -65.37 -70.90 11.98 0.86 -63.30 159.09 19.76
35 109D 109D N CA 873 874 160.93 150.30 -40.00
36 4422 110R 111G C N 890 892 84.80 78.70 45.91 1.06 -62.40 -134.83 31.25
36 111G 111G N CA 892 893 148.40 -166.10 -41.20
37 4442 130A 131G C N 1039 1041 49.18 78.70 29.57 1.53 -62.40 168.68 23.46
37 131G 131G N CA 1041 1042 -167.71 -166.10 -41.20
38 4443 131G 132Y C N 1043 1045 -173.31 -124.30 50.41 4.07 -63.50 -160.09 27.63
38 132Y 132Y N CA 1045 1046 123.65 135.40 -43.40
39 4446 134Q 135F C N 1068 1070 -120.15 -124.20 47.30 2.32 -63.20 137.61 22.80
39 135F 135F N CA 1070 1071 -169.58 143.30 -44.30
40 4456 144A 145K C N 1147 1149 -51.64 -62.90 26.22 3.01 -118.00 169.92 8.79
40 145K 145K N CA 1149 1150 -64.48 -40.80 139.10
41 4457 145K 146F C N 1156 1158 -111.60 -124.20 70.39 2.98 -63.20 127.87 14.97
41 146F 146F N CA 1158 1159 74.05 143.30 -44.30
42 4461 149A 150G C N 1190 1192 78.28 82.20 4.94 0.18 -62.40 150.24 28.30
42 150G 150G N CA 1192 1193 11.52 8.50 -41.20
43 4462 150G 151G C N 1194 1196 68.72 82.20 27.05 0.75 -62.40 150.15 28.40
43 151G 151G N CA 1196 1197 31.96 8.50 -41.20
44 4465 153V 154R C N 1212 1214 -47.15 -63.00 22.24 2.64 -72.10 163.33 13.09
44 154R 154R N CA 1214 1215 -56.69 -41.10 141.90
45 4466 154R 155E C N 1223 1225 -87.49 -117.80 86.41 3.65 -63.60 99.10 12.06
45 155E 155E N CA 1225 1226 55.88 136.80 -40.30
46 4467 155E 156I C N 1232 1234 -89.53 -120.60 42.21 3.36 -63.40 159.68 27.12
46 156I 156I N CA 1234 1235 158.87 130.30 -43.60
47 4468 156I 157D C N 1240 1242 -71.98 -63.30 10.36 1.29 54.50 147.16 19.08
47 157D 157D N CA 1242 1243 -34.33 -40.00 40.90
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 35 35 125 145 210 166 206 250 236 286
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
LYS_LAMBD.B99990001.pdb 1328.08752
import __main__
__main__.pymol_argv = [ 'pymol', '-x' ]
import pymol
pymol.finish_launching()
from pymol import cmd
from IPython.display import Image
pymol.cmd.reinitialize()
pymol.cmd.do('''
load LYS_LAMBD.B99990001.pdb
load template.pdb
hide nonbonded
align template, LYS_LAMBD.B99990001
orient LYS_LAMBD.B99990001
zoom LYS_LAMBD.B99990001
ray
png pic0.png
''')
Image(filename='pic0.png')
Остов структуры окружением активного центра похож на изначальный вариант, поменялись только окружающие петли. Правдоподобно, я считаю.
Переместим лиганд...
class mymodel(modeller.automodel.automodel):
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
for x,y in [('N:20:A','N:96:A')]:
rsr.add(modeller.forms.gaussian(group=modeller.physical.xy_distance,
feature=modeller.features.distance(
at[x],at[y]),mean=3.0, stdev=0.1))
s = alignm[0]
pdb = alignm[1]
a1 = mymodel(env, alnfile='a_lig.ali', knowns=pdb.code, sequence=s.code)
a1.name='mod'+s.code
a1.starting_model = 1
a1.ending_model = 1
a1.make()
automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead
read_pd_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.
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.
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.)
The following 1 residues contain 6-membered rings with poor geometries
after transfer from templates. Rebuilding rings from internal coordinates:
<Residue 45:A (type TYR)>
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
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
distance___W> The class 'distance' is deprecated; use 'Distance' instead
gaussian___W> The class 'gaussian' is deprecated; use 'Gaussian' instead
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 13525 12409
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
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 : 161
Number of all, selected real atoms : 1300 1300
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12409 12409
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3789
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 : 2188.3728
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 : 1282 0 2 0.009 0.009 26.344 1.000
2 Bond angle potential : 1726 2 16 2.711 2.711 252.96 1.000
3 Stereochemical cosine torsion poten: 789 0 37 50.848 50.848 312.17 1.000
4 Stereochemical improper torsion pot: 515 0 0 1.520 1.520 24.571 1.000
5 Soft-sphere overlap restraints : 3789 1 2 0.008 0.008 28.124 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) : 2407 14 52 0.838 0.838 478.80 1.000
10 Distance restraints 2 (N-O) : 2568 7 57 0.822 0.822 503.17 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: 157 3 16 7.607 7.607 107.14 1.000
14 Sidechain Chi_1 dihedral restraints: 130 0 3 84.524 84.524 59.398 1.000
15 Sidechain Chi_2 dihedral restraints: 107 0 0 80.519 80.519 51.375 1.000
16 Sidechain Chi_3 dihedral restraints: 48 0 0 81.941 81.941 30.699 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 98.967 98.967 15.082 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 941 0 0 0.449 0.449 21.991 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: 156 51 37 38.209 96.607 179.11 1.000
26 Distance restraints 4 (SDCH-SDCH) : 157 0 2 1.304 1.304 32.331 1.000
27 Distance restraints 5 (X-Y) : 1402 1 1 0.052 0.052 65.116 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: LYS_LAMBD.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: 26376.9238
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 2339 95A 95A N CA 765 766 136.17 107.00 29.17 8.39 107.00 29.17 8.39
2 2341 95A 95A CA C 766 768 132.32 116.50 15.82 4.55 116.50 15.82 4.55
-------------------------------------------------------------------------------------------------
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 6147 52L 95A CA CA 417 766 7.74 4.75 2.99 5.56 4.75 2.99 5.56
-------------------------------------------------------------------------------------------------
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 7696 20G 16A N O 160 130 9.35 4.30 5.04 6.59 4.30 5.04 6.59
2 7774 36I 17W N O 287 144 8.23 4.62 3.61 5.79 4.62 3.61 5.79
-------------------------------------------------------------------------------------------------
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 4504 36I 36I CA C 288 293 -156.88 -180.00 23.12 4.62 -180.00 23.12 4.62
2 4563 95A 95A CA C 766 768 -137.06 -180.00 42.94 8.59 -180.00 42.94 8.59
-------------------------------------------------------------------------------------------------
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 4327 15L 16A C N 124 126 82.25 55.40 49.81 1.94 -62.50 149.44 29.95
1 16A 16A N CA 126 127 -3.75 38.20 -40.90
2 4328 16A 17W C N 129 131 -134.83 -124.90 64.99 3.37 -63.00 142.76 15.76
2 17W 17W N CA 131 132 79.18 143.40 -44.20
3 4330 18S 19E C N 149 151 124.71 -117.80 118.03 4.06 -63.60 -117.24 41.14
3 19E 19E N CA 151 152 148.08 136.80 -40.30
4 4333 21T 22D C N 169 171 -57.05 -70.90 13.86 1.07 54.50 156.68 9.65
4 22D 22D N CA 171 172 150.93 150.30 40.90
5 4335 23N 24G C N 185 187 -101.87 -80.20 38.96 0.96 82.20 -120.83 7.84
5 24G 24G N CA 187 188 -153.52 174.10 8.50
6 4336 24G 25R C N 189 191 64.69 57.30 25.01 2.21 -63.00 164.05 29.74
6 25R 25R N CA 191 192 61.89 38.00 -41.10
7 4337 25R 26Q C N 200 202 -67.60 -73.00 11.24 0.65 -63.80 171.19 24.97
7 26Q 26Q N CA 202 203 130.84 140.70 -40.30
8 4338 26Q 27K C N 209 211 -160.96 -118.00 43.61 1.53 -62.90 -161.50 31.63
8 27K 27K N CA 211 212 146.61 139.10 -40.80
9 4339 27K 28T C N 218 220 -97.42 -78.10 41.13 1.34 -63.20 136.16 19.74
9 28T 28T N CA 220 221 -173.89 149.80 -42.10
10 4340 28T 29R C N 225 227 -91.00 -72.10 22.38 1.47 -63.00 167.37 24.54
10 29R 29R N CA 227 228 153.89 141.90 -41.10
11 4341 29R 30N C N 236 238 -139.61 -119.90 73.42 2.85 -63.20 134.91 21.05
11 30N 30N N CA 238 239 -152.28 137.00 -41.10
12 4342 30N 31H C N 244 246 -111.43 -125.60 16.07 0.42 -63.20 -179.91 19.98
12 31H 31H N CA 246 247 131.21 138.80 -42.30
13 4344 32G 33Y C N 258 260 -115.91 -124.30 9.73 0.53 -63.50 -178.40 26.36
13 33Y 33Y N CA 260 261 130.47 135.40 -43.40
14 4345 33Y 34D C N 270 272 -126.28 -96.50 41.48 1.73 -63.30 -172.19 27.25
14 34D 34D N CA 272 273 143.06 114.20 -40.00
15 4347 35V 36I C N 285 287 -94.25 -120.60 34.79 1.54 -63.40 154.31 24.30
15 36I 36I N CA 287 288 107.59 130.30 -43.60
16 4358 46S 47D C N 369 371 -155.81 -96.50 97.37 4.01 -63.30 120.35 14.13
16 47D 47D N CA 371 372 36.98 114.20 -40.00
17 4359 47D 48H C N 377 379 62.84 -67.60 137.20 11.50 56.30 141.89 13.11
17 48H 48H N CA 379 380 -177.46 140.00 40.80
18 4360 48H 49P C N 387 389 -79.17 -58.70 55.56 3.31 -64.50 126.90 10.26
18 49P 49P N CA 389 390 21.15 -30.50 147.20
19 4379 67Y 68Q C N 534 536 59.77 55.10 14.49 1.44 -121.10 -161.43 9.27
19 68Q 68Q N CA 536 537 54.02 40.30 139.70
20 4388 76A 77Y C N 617 619 -120.59 -63.50 84.56 11.71 -63.50 84.56 11.71
20 77Y 77Y N CA 619 620 18.98 -43.40 -43.40
21 4390 78R 79K C N 640 642 -149.18 -118.00 94.33 4.86 -62.90 125.31 15.10
21 79K 79K N CA 642 643 50.07 139.10 -40.80
22 4395 83L 84K C N 678 680 -130.01 -118.00 89.51 4.49 -62.90 113.23 13.21
22 84K 84K N CA 680 681 50.40 139.10 -40.80
23 4396 84K 85D C N 687 689 -33.76 -96.50 68.67 2.84 54.50 99.25 8.47
23 85D 85D N CA 689 690 86.29 114.20 40.90
24 4398 86F 87S C N 706 708 -101.64 -72.40 81.94 5.81 -64.10 117.04 7.21
24 87S 87S N CA 708 709 75.86 152.40 -35.00
25 4405 93A 94V C N 756 758 -69.23 -125.40 69.34 1.83 -62.40 145.20 17.99
25 94V 94V N CA 758 759 102.64 143.30 -42.40
26 4407 95A 96L C N 768 770 -43.13 -70.70 31.80 2.28 -63.50 168.19 24.57
26 96L 96L N CA 770 771 125.75 141.60 -41.20
27 4408 96L 97Q C N 776 778 -163.04 -121.10 94.43 3.63 -63.80 137.66 24.82
27 97Q 97Q N CA 778 779 -135.70 139.70 -40.30
28 4409 97Q 98Q C N 785 787 -90.70 -73.00 27.15 1.56 -63.80 160.67 25.06
28 98Q 98Q N CA 787 788 161.30 140.70 -40.30
29 4411 99I 100K C N 802 804 -153.52 -118.00 40.28 1.88 -62.90 -175.33 21.23
29 100K 100K N CA 804 805 120.10 139.10 -40.80
30 4412 100K 101E C N 811 813 -171.89 -117.80 61.13 1.79 -63.60 -171.41 31.01
30 101E 101E N CA 813 814 165.29 136.80 -40.30
31 4413 101E 102R C N 820 822 -127.54 -125.20 15.95 0.82 -63.00 178.02 20.60
31 102R 102R N CA 822 823 124.82 140.60 -41.10
32 4414 102R 103G C N 831 833 76.95 78.70 22.65 0.72 82.20 162.90 7.64
32 103G 103G N CA 833 834 171.32 -166.10 8.50
33 4415 103G 104A C N 835 837 -133.52 -134.00 5.80 0.32 -62.50 -168.46 35.19
33 104A 104A N CA 837 838 141.22 147.00 -40.90
34 4416 104A 105L C N 840 842 -115.65 -108.50 13.86 0.66 -63.50 -177.95 28.49
34 105L 105L N CA 842 843 144.38 132.50 -41.20
35 4417 105L 106P C N 848 850 -52.37 -58.70 10.38 0.65 -64.50 174.50 13.67
35 106P 106P N CA 850 851 -38.72 -30.50 147.20
36 4418 106P 107M C N 855 857 -108.62 -125.60 17.75 0.58 -63.40 -178.48 23.97
36 107M 107M N CA 857 858 135.29 140.50 -40.50
37 4420 108I 109D C N 871 873 -83.71 -70.90 27.01 0.90 -63.30 147.35 19.48
37 109D 109D N CA 873 874 174.07 150.30 -40.00
38 4422 110R 111G C N 890 892 129.21 82.20 62.99 2.10 -62.40 168.57 29.79
38 111G 111G N CA 892 893 -33.43 8.50 -41.20
39 4442 130A 131G C N 1039 1041 55.59 78.70 40.05 2.00 -62.40 -163.12 27.01
39 131G 131G N CA 1041 1042 161.20 -166.10 -41.20
40 4443 131G 132Y C N 1043 1045 144.96 -124.30 107.29 8.90 -63.50 -165.74 27.49
40 132Y 132Y N CA 1045 1046 78.15 135.40 -43.40
41 4444 132Y 133G C N 1055 1057 -73.13 -62.40 10.73 1.91 82.20 163.03 12.33
41 133G 133G N CA 1057 1058 -41.01 -41.20 8.50
42 4445 133G 134Q C N 1059 1061 -163.13 -121.10 78.39 4.10 -63.80 151.08 19.51
42 134Q 134Q N CA 1061 1062 73.53 139.70 -40.30
43 4446 134Q 135F C N 1068 1070 -141.32 -124.20 85.89 3.59 -63.20 117.85 20.92
43 135F 135F N CA 1070 1071 -132.53 143.30 -44.30
44 4456 144A 145K C N 1147 1149 -51.59 -62.90 23.52 2.70 -118.00 172.75 8.94
44 145K 145K N CA 1149 1150 -61.42 -40.80 139.10
45 4457 145K 146F C N 1156 1158 -113.40 -124.20 64.19 2.74 -63.20 134.08 15.72
45 146F 146F N CA 1158 1159 80.03 143.30 -44.30
46 4461 149A 150G C N 1190 1192 82.26 82.20 0.89 0.05 -62.40 153.25 28.82
46 150G 150G N CA 1192 1193 9.39 8.50 -41.20
47 4462 150G 151G C N 1194 1196 69.17 82.20 24.46 0.67 -62.40 149.22 28.22
47 151G 151G N CA 1196 1197 29.20 8.50 -41.20
48 4465 153V 154R C N 1212 1214 -49.11 -63.00 19.70 2.33 -72.10 164.65 13.15
48 154R 154R N CA 1214 1215 -55.06 -41.10 141.90
49 4466 154R 155E C N 1223 1225 -90.58 -117.80 83.78 3.60 -63.60 101.52 12.26
49 155E 155E N CA 1225 1226 57.56 136.80 -40.30
50 4467 155E 156I C N 1232 1234 -99.33 -120.60 23.12 1.82 -63.40 -179.35 30.92
50 156I 156I N CA 1234 1235 139.36 130.30 -43.60
51 4468 156I 157D C N 1240 1242 -94.78 -96.50 53.81 2.26 54.50 150.55 16.61
51 157D 157D N CA 1242 1243 60.42 114.20 40.90
-------------------------------------------------------------------------------------------------
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 12409 20G 96L N N 160 770 4.25 3.00 1.25 12.46 3.00 1.25 12.46
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 30 43 156 172 194 191 219 268 242 280
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
LYS_LAMBD.B99990001.pdb 2188.37280
pymol.cmd.reinitialize()
pymol.cmd.do('''
load LYS_LAMBD.B99990002.pdb
load template.pdb
hide nonbonded
align template, LYS_LAMBD.B99990002
orient LYS_LAMBD.B99990002
zoom LYS_LAMBD.B99990002
ray
png pic0.png
''')
Image(filename='pic0.png')
pymol.cmd.reinitialize()
pymol.cmd.do('''
load LYS_LAMBD.B99990002.pdb
load LYS_LAMBD.B99990001.pdb
hide nonbonded
align LYS_LAMBD.B99990001, LYS_LAMBD.B99990002
orient LYS_LAMBD.B99990002
zoom LYS_LAMBD.B99990002
ray
png pic0.png
''')
Image(filename='pic0.png')
Лиганд там же, но белок немного изменился - те самые петли немного сдвинулись. Думаю, это вообще не принципиально.
Заменим все на аланин:
alignm = modeller.alignment(env)
mdl = modeller.model(env, file='template.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
alignm.append_model(mdl, atom_files='template.pdb', align_codes='template')
seq_ala = 'A' * 129 + '...'
alignm.append_sequence(seq_ala)
alignm[0].code = '1lmp'
alignm[1].code = 'ala'
alignm.salign()
alignm.write(file='b.ali', alignment_format='PIR')
! sed -i 's/129/132/g' b.ali
! sed -i 's/---/.../g' b.ali
! cat b.ali
alignment__W> The class 'alignment' is deprecated; use 'Alignment' instead model______W> The class 'model' is deprecated; use 'Model' instead SALIGN_____> adding the next group to the alignment; iteration 1 >P1;1lmp structureX:template.pdb:1:A:+132:A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWCDDGRTPGAKNV CGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...* >P1;ala sequence::1:A:+132:A:undefined:undefined:-1.00:-1.00 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA...*
s = alignm[1]
pdb = alignm[0]
a = modeller.automodel.automodel(env, alnfile='b.ali', knowns= pdb.code , sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 1
a.make()
automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead
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: 1 129
atom names : C +N
atom indices : 644 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 1 129
atom names : C CA +N O
atom indices : 644 642 0 645
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.)
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: 10115 9477
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 132
Number of all, selected real atoms : 689 689
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9477 9477
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1197
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 : 575.5462
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 : 645 0 0 0.006 0.006 6.6732 1.000
2 Bond angle potential : 902 0 5 2.324 2.324 99.184 1.000
3 Stereochemical cosine torsion poten: 262 0 32 77.082 77.082 250.32 1.000
4 Stereochemical improper torsion pot: 258 0 0 0.953 0.953 6.2614 1.000
5 Soft-sphere overlap restraints : 1197 2 2 0.011 0.011 16.615 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2404 0 0 0.195 0.195 44.330 1.000
10 Distance restraints 2 (N-O) : 2562 0 0 0.270 0.270 75.915 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: 128 1 3 5.071 5.071 38.816 1.000
14 Sidechain Chi_1 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 726 0 0 0.220 0.220 4.7993 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: 127 18 10 26.048 59.954 15.911 1.000
26 Distance restraints 4 (SDCH-SDCH) : 62 0 0 0.358 0.358 0.93739 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.034 0.034 15.788 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: ala.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: 10706.2490
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 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 2318 124A 124A CA C 617 619 -155.54 -180.00 24.46 4.89 -180.00 24.46 4.89
-------------------------------------------------------------------------------------------------
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 2082 15A 16A C N 74 76 78.80 55.40 26.76 2.02 -62.50 156.00 31.70
1 16A 16A N CA 76 77 25.22 38.20 -40.90
2 2085 18A 19A C N 89 91 65.75 55.40 24.08 0.87 -62.50 140.48 28.53
2 19A 19A N CA 91 92 16.45 38.20 -40.90
3 2087 20A 21A C N 99 101 54.45 55.40 6.09 0.45 -62.50 137.91 28.03
3 21A 21A N CA 101 102 32.19 38.20 -40.90
4 2088 21A 22A C N 104 106 58.32 55.40 3.02 0.29 -62.50 144.01 29.25
4 22A 22A N CA 106 107 37.46 38.20 -40.90
5 2103 36A 37A C N 179 181 65.92 55.40 13.47 0.83 -62.50 146.58 29.81
5 37A 37A N CA 181 182 29.79 38.20 -40.90
6 2104 37A 38A C N 184 186 63.67 55.40 13.43 0.59 -62.50 143.57 29.20
6 38A 38A N CA 186 187 27.62 38.20 -40.90
7 2115 48A 49A C N 239 241 87.79 55.40 44.99 2.44 -62.50 157.73 31.80
7 49A 49A N CA 241 242 6.98 38.20 -40.90
8 2120 53A 54A C N 264 266 87.95 -134.00 143.24 3.52 -62.50 -158.60 31.55
8 54A 54A N CA 266 267 -174.79 147.00 -40.90
9 2123 56A 57A C N 279 281 60.68 55.40 12.37 1.17 -62.50 152.72 30.94
9 57A 57A N CA 281 282 49.38 38.20 -40.90
10 2133 66A 67A C N 329 331 81.44 55.40 58.76 2.13 -62.50 146.35 29.07
10 67A 67A N CA 331 332 -14.47 38.20 -40.90
11 2137 70A 71A C N 349 351 50.69 55.40 18.71 0.78 -62.50 149.19 30.05
11 71A 71A N CA 351 352 56.30 38.20 -40.90
12 2140 73A 74A C N 364 366 53.75 55.40 19.60 1.05 -62.50 152.45 30.73
12 74A 74A N CA 366 367 57.73 38.20 -40.90
13 2143 76A 77A C N 379 381 66.57 55.40 11.18 1.24 -62.50 151.64 30.82
13 77A 77A N CA 381 382 38.69 38.20 -40.90
14 2170 103A 104A C N 514 516 82.58 -134.00 159.08 3.62 -62.50 178.08 28.71
14 104A 104A N CA 516 517 -144.18 147.00 -40.90
15 2183 116A 117A C N 579 581 51.08 55.40 9.29 0.34 -62.50 143.27 28.99
15 117A 117A N CA 581 582 46.43 38.20 -40.90
16 2191 124A 125A C N 619 621 -50.66 -62.50 15.10 2.40 -68.20 165.35 13.95
16 125A 125A N CA 621 622 -50.28 -40.90 145.30
17 2192 125A 126A C N 624 626 -102.94 -62.50 85.63 12.83 -62.50 85.63 12.83
17 126A 126A N CA 626 627 34.58 -40.90 -40.90
18 2194 127A 128A C N 634 636 62.71 55.40 9.85 0.56 -62.50 144.68 29.42
18 128A 128A N CA 636 637 31.59 38.20 -40.90
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 2 3 31 47 62 60 80 110 100 82
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
ala.B99990001.pdb 575.54620
pymol.cmd.reinitialize()
pymol.cmd.do('''
load ala.B99990001.pdb
load template.pdb
hide nonbonded
align template, ala.B99990001
orient ala.B99990001
zoom ala.B99990001
ray
png pic0.png
''')
Image(filename='pic0.png')
Структурно скелет аланинового лизоцима идентичен нативному. У аланина хватает подвижности на весь ход цепи - а большего алгоритму и не надо))