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/...*