Dear all
My name is Sergio Garay and I am pretty new using modeller so it is
probable that my questions can be "a little" silly. I am trying to
build a model with two kind of restrictions (using a multiple templates
alignment): a disulphide bridge and the position of ligands. I was able
to obtain (following your tutorial) models with each restriction applied
in a separate way. The problem appear (errors) when I try to combine both
restriction at the same time. I am using mod9v6, and I follow the examples
of
that version. Is there any problem in my py script?
Any help will be appreciated.
*Below I've pasted the python script that I used*:
# Homology modeling by the automodel class
from modeller import * # Load standard Modeller classes
from modeller.automodel import * # Load the automodel class
# Redefine the special_patches routine to include the additional disulfides
# (this routine is empty by default):
class MyModel(automodel):
def special_patches(self, aln):
# A disulfide between residues 345 and 668:
self.patch(residue_type='DISU', residues=(self.residues['345'],
self.residues['668']))
log.verbose() # request verbose output
env = environ() # create a new MODELLER environment to build this model in
# directories for input atom files
env.io.atom_files_directory = './:../atom_files'
# Read in HETATM records from template PDBs
env.io.hetatm = True
a = MyModel(env,
alnfile = 'alignment.ali', # alignment filename
knowns = ('2ioaB_amidase', '2vobB', '2ioaB_sinthetase'), #
codes of the templates
sequence = 'tcruzi') # code of the target
a.starting_model= 3 # index of the first model
a.ending_model = 3 # index of the last model
# (determines how many models to
calculate)
a.make() # do the actual homology modeling
*The error in the terminal: *
Traceback (most recent call last):
File "model-mixed.py", line 30, in ?
a.make() # do the actual homology modeling
File "/usr/lib/modeller9v6/modlib/modeller/automodel/automodel.py", line
98, in make
self.homcsr(exit_stage)
File "/usr/lib/modeller9v6/modlib/modeller/automodel/automodel.py", line
427, in homcsr
self.make_initial_model(aln)
File "/usr/lib/modeller9v6/modlib/modeller/automodel/automodel.py", line
441, in make_initial_model
self.generate_method(self, aln)
File "/usr/lib/modeller9v6/modlib/modeller/automodel/generate.py", line
25, in transfer_xyz
mdl.create_topology(aln)
File "/usr/lib/modeller9v6/modlib/modeller/automodel/automodel.py", line
659, in create_topology
self.special_patches(aln)
File "model-mixed.py", line 10, in special_patches
self.patch(residue_type='DISU', residues=(self.residues['345'],
File "/usr/lib/modeller9v6/modlib/modeller/coordinates.py", line 226, in
__getitem__
(self.offset, self.length, self.suffix))
File "/usr/lib/modeller9v6/modlib/modeller/util/modutil.py", line 19, in
handle_seq_indx
int_indx = lookup_func(*args)
File "/usr/lib/modeller9v6/modlib/modeller/coordinates.py", line 283, in
_indxres
raise KeyError("No such residue: %s" % indx)
KeyError: 'No such residue: 345'
*The log file write by Modeller:*
MODELLER 9v6, 2009/01/30, r6593
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2009 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, 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
leichmania.unl.edu.ar2.6.26.8-57.fc8 x86_64
Date and time of compilation : 2009/01/30 23:00:55
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2009/03/05 07:20:23
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL9v6}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL9v6}/modlib/sstruc.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234076
3158.277 3.084
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234604
3158.793 3.085
openf___224_> Open ${MODINSTALL9v6}/modlib/resdih.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283204
3206.254 3.131
rdrdih__263_> Number of dihedral angle types : 9
Maximal number of dihedral angle optima: 3
Dihedral angle names : Alph Phi Psi Omeg
chi1 chi2 chi3 chi4 chi5
openf___224_> Open ${MODINSTALL9v6}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292444
3215.277 3.140
openf___224_> Open ${MODINSTALL9v6}/modlib/radii14.lib
openf___224_> Open ${MODINSTALL9v6}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL9v6}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL9v6}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL9v6}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL9v6}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL9v6}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types: 21
io_data____W> Setting io.atom_files_directory to a colon-delimited string is
deprecated, as it is not robust on Windows systems. Set it to
a list of directories instead. For example:
env.io.atom_files_directory = ['./', '../atom_files']
openf___224_> Open alignment.ali
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3303901
3226.466 3.151
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3305351
3227.882 3.152
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3308251
3230.714 3.155
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3314051
3236.378 3.161
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3325651
3247.706 3.172
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3554183
3470.882 3.390
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3554211
3470.909 3.390
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3554239
3470.937 3.390
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3554267
3470.964 3.390
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3554295
3470.991 3.390
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3555003
3471.683 3.390
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3557363
3473.987 3.393
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3559015
3475.601 3.394
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3561899
3478.417 3.397
read_al_374_> Non-standard residue type,position,sequence: .
739 3
read_al_374_> Non-standard residue type,position,sequence: .
740 3
read_al_374_> Non-standard residue type,position,sequence: .
741 3
read_al_374_> Non-standard residue type,position,sequence: .
739 4
read_al_374_> Non-standard residue type,position,sequence: .
740 4
read_al_374_> Non-standard residue type,position,sequence: .
741 4
Read the alignment from file : alignment.ali
Total number of alignment positions: 741
# Code #_Res #_Segm PDB_code Name
-------------------------------------------------------------------------------
1 2ioaB_ami 178 1 2ioaB_amida
2 2vobB 591 1 2vobB
3 2ioaB_sin 414 2 2ioaB_sinth
4 tcruzi 722 2 tcruzi
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open ./2ioaB_amidase.pdb
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 3665465
3579.556 3.496
openf___224_> Open ./2vobB.pdb
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 4011534
3917.514 3.826
openf___224_> Open ./2ioaB_sinthetase.pdb
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 4253508
4153.816 4.056
replace_706W> BLK ('.') residue type in alignment will force 'automodel'
model building to treat residue type MG as a rigid body,
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, use 1-letter code ' $' in the alignment.
replace_706W> BLK ('.') residue type in alignment will force 'automodel'
model building to treat residue type MG as a rigid body,
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, use 1-letter code ' $' in the alignment.
replace_706W> BLK ('.') residue type in alignment will force 'automodel'
model building to treat residue type ADP as a rigid body,
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, use 1-letter code ' &' in the alignment.
fndatmi_285W> Only 411 residues out of 414 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 pairwise structural superpositions.
Equivalent CA pairs with distance difference larger than 6.0 angstroms:
ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------------
drmsq1__W> n<2
drmsq3__W> n<2
248 2 3 215 204 P I 7.832
249 2 3 216 205 P A 6.141
371 2 3 335 324 N R 6.155
405 2 3 368 356 G G 6.617
407 2 3 370 357 D N 6.545
508 2 3 466 451 D I 6.965
509 2 3 467 452 Y R 6.999
524 2 3 477 464 N I 10.068
530 2 3 482 469 P P 7.125
588 2 3 539 525 E L 6.179
592 2 3 543 529 H G 6.116
596 2 3 547 533 K K 7.078
601 2 3 578 536 R A 15.389
667 2 3 579 565 N N 6.052
707 2 3 617 605 S I 6.995
END OF TABLE
fndatmi_285W> Only 411 residues out of 414 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 target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
45 1 31 43 R I 15.730
288 2 250 265 G F 19.941
513 3 454 459 A W 9.670
600 2 551 578 G R 11.251
721 2 632 637 R Q 14.815
END OF TABLE
check_a_344_> << END OF COMMAND
openf___224_> Open ${LIB}/top_heav.lib
read_to_681_> topology.submodel read from topology file: 3
openf___224_> Open ${MODINSTALL9v6}/modlib/models.lib
openf___224_> Open ${LIB}/par.lib
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 5202292
5080.363 4.961
openf___224_> Open ${LIB}/par.lib
read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE
227 561 661 112 0
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5315018
5190.447 5.069
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5876166
5738.443 5.604
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5963014
5823.256 5.687
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 18 719
atom names : C +N
atom indices : 5706 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 18 719
atom names : C CA +N O
atom indices : 5706 5702 0 5707
mkilst______> segment topology constructed from sequence and RTF:
segments residues atoms bonds angles dihedrals impropers:
1 719 5707 5854 0 0 2501
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 6209366
6063.834 5.922
patch_______> segment topology patched using RTF: 1 ; MET ; NTER
segments residues atoms bonds angles dihedrals impropers:
1 719 5707 5854 7949 9437 2501
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 6484142
6332.170 6.184
patch_______> segment topology patched using RTF: 719 ; VAL ; CTER
segments residues atoms bonds angles dihedrals impropers:
1 719 5708 5855 7951 9439 2502
genseg______> segment topology constructed from sequence and RTF:
segments residues atoms bonds angles dihedrals impropers:
1 719 5708 5855 7951 9439 2502
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 6484170
6332.197 6.184
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 6484641
6332.657 6.184
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 6486699
6334.667 6.186
mkilst______> segment topology constructed from sequence and RTF:
segments residues atoms bonds angles dihedrals impropers:
2 722 5737 5855 7951 9439 2502
genseg______> segment topology constructed from sequence and RTF:
segments residues atoms bonds angles dihedrals impropers:
2 722 5737 5855 7951 9439 2502
fndatmi_285W> Only 411 residues out of 414 contain atoms of type
CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
*The alignmet used:
*
>P1; 2ioaB_amidase
structureX:2ioaB_amidase:12:B:200:B:::-1.00:-1.00
-------------------FGTLLGYAPGGVAIYSSD---Y---SV--------------
FRSYIDDEYMGHKWQCVEFARRFLFLNYGVVFTDVGMAWEIFSLRFLREVVND-NILPLQ
AFPNGSPRAPVAGALLIWDKGGEFKDTGHVAIITQLHGNKVRIAEQNVIHSPLPQGQQWT
RELEMVVEN-GCYTLKD-TFD-D-TTILGWMIQTEDTEYSLP------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
-------------------/---*
>P1; 2vobB
structureX:2vobB:5:B:652:B:::-1.00:-1.00
-----QRASVSFNKPGHIPFGAVQGYAPGGVPAYSNKHDHYFSG----------------
ERNIEDNIFFGFKYQCVEFARRWLLVRKGLLLPDVNWACHIFQLKEVRDAATT-ESFAVL
QVRNGTTTKPEADALLVYPSTDAN-PVGHVGTITEVGDDYVCVADQNYRFHKWE--SSCA
YKLKLDHRD-GIWTIIDDIDADEIEIPLGWLTFP--------GRANRPEGAPPVALHPSL
HFKE---PP--KPYLLRRNF-LPW--------LDMNNPAERLFVEEFG----------VS
YYESNHEFHLRCVAYGTQLHAIFMEATAQVIESDEKLRLFAIPEEFWPRIRHSWKYQQ-T
YISGRFDFAFNNETGEVKCFEYNADSASTLLECGLIQQKWAESV-GLDDTRGSGFAVERN
LKMAWANSG------ATGRVHFCVDEEREEQYTALYCMQAAEAVGLEGKLCILFDEFRF-
DDNGHVVDSDGVRVRNVWKTWMWESAITDYYAAR-----EERGEN-WKPSPK-DKVRLCD
LLLGDDWEILYFEPMWKVIPSNKAILPMIYHNHPEHPAILKAEYELTDELRKHGYAKKPI
VR----------------------------------------------------------
-------NMIYQQLFELKKQDDYYAIIGGWMIGDAFSGTGIREDK--S-----PFAAVRI
-KPHPVTLKDIDKMAEDE-/---*
>P1; 2ioaB_sinthetase
structureX:2ioaB_sinthetase:201:B:621:B:::-1.00:-1.00
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
----QPEIAGELLKISGARLEN--KGQFDGKWLDEKDPLQNAYVQAN--GQVINQDPYHY
YTITESAEQELIKATNELHLMYLHATDKVLKDDNLLALFDIPKILWPRLRLSWQRRRHHM
ITGRMDFCMDER--GLKVYEYNADSASCHTEAGLILERWAEQGYKG-NGFNPAEGLINEL
AGAWKHSRA------RPFVHIMQDKDIEENYHAQFMEQALHQAGFETRILRGLDELGW--
G--QLIDGEGRLVNCVWKTWAWETAFDQIRE--VFAAVP-----IR-TGHPQNEVRLIDV
LLR--PEVLVFEPLWTVIPGNKAILPILWSLFPHHRYLLDTDFTVNDELVKTGYAVKPI-
-AGRCGSNIDLVSHH-------------------------------------EEVLDKTS
GKFAEQKNIYQQLWCLPKVDGKYIQVCTFTVGGNYGGTCLRGDESLVIKKESDIEPLIVV
K------------------/...*
>P1; tcruzi
sequence:tcruzi:::::::0.00:0.00
MENTDKQRGVHASETEHVSFGGVIGVTDCGVPVFSNGEKKFFSERISFAPDCKRVEAAAP
TTVIGTHDTLGYKWLCLEFARRYLLMTKGVWLASVPTAEDIWEIDEIVTSVPIGTPVPVE
REKHGDTTSMPSVGDLLVWSRTEDSPYGHLAVVTHVSDNGVCVAEQNYEFKRWQEGKNYS
RRFDCEKREDGVTVFVGETHLLGWVIIKAPPYDFSLGDLPDKYRHIIGPGHIVRRHLEKD
VLLPWLNPSQRCDFFLKRSLTVG--------GYMGEDAVAEAHSVPDG------------
FYMMDYDMWCRFRFATKNLHAVAVEATRLILNSRDSEALLVQYFGLPKELHLQLRRSFET
IPSMCGRFDFGYDGKEIIMLAYNCDSSAAMLECGDTQEKFARHYGVELGTSTGSFLYSRI
ANYFNCLIQNEFLCPHHKIVHFMIDDDDEERYTALYVMNAAESAGFRTKLCVKLSGFRFG
STTGEVDRDASPTERRSVVDLENEEVLLVWKTWAWDTVLRQYVEQRTQQGHGVSTKPTLS
DILLNEHIRVLEPLWKAVTGSKAILPFMYAAAPHHSNMVPASFYRTKEIISAPYLTKPVN
GRSGKSMTMYDTGEDPEAVAAAPHTAAAPVLGRSISAVLFDDAPAGTYRVPFDNIQENLT
ERLFDSVVVYQSRVFLTRYEKKYSPIFCGWNVGGEFGGVIVREENFNNTKLSSLVIPSRV
VRQHIPLHAMQESTTSGEV/...*
--
Dr. Sergio Garay
Facultad de Bioquimica y Cs. Biológicas
Universidad Nacional del Litoral
Santa Fe - Argentina
C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
Argentina
Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221
