[modeller_usage] Problem applying two different restrictions....
To:
Subject: [modeller_usage] Problem applying two different restrictions....
From: Sergio Garay <>
Date: Thu, 5 Mar 2009 06:18:34 -0500
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.ar 2.6.26.8-57.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 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.)
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
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.)
-- 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