May 2002 - modeller_usage

Adding residues
by Dan Thomas Major 03 May '02

03 May '02

I want to add missing residues to a pdb file using modeller without changing existing coordinates. I try select the wanted residues with the select_atoms subroutine, but it seems to me that it changes the coordinates of other residues as well, not just the ones selected. Thanks, Dan Below is the top file: ############################################################################## # Modeller script to add missing residues in rhodopsin X-ray structure # ############################################################################## SET OUTPUT_CONTROL = 1 1 1 1 1 INCLUDE # Include the predefined TOP routines READ_ALIGNMENT FILE = '1HZX-1HZX.ali', ALIGN_CODES = '1HZXA' '1HZXA2' SET ALNFILE = '1HZX-1HZX.ali' # alignment filename SET KNOWNS = '1HZXA' # codes of the templates SET SEQUENCE = '1HZXA2' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files DESCRIBE ############################################################################## # Thorough homology modelling by the MODELLER TOP routine 'model'. # Initial model read from file and not from template SET OUTPUT = 'LONG' SET STARTING_MODEL = 1 SET ENDING_MODEL = 1 ############### # Do modeling # ############### CALL ROUTINE = 'very_fast' # prepare for extremely fast optimization CALL ROUTINE = 'model' # do homology modelling ############################################################################## ############################################################################## # Select missing loop coordinates for modelling SUBROUTINE ROUTINE = 'select_atoms' # Missing segment 235-241 PICK_ATOMS SELECTION_SEGMENT = '236:' '240:', SELECTION_SEARCH = 'segment',; SELECTION_STATUS = 'initialize' # Missing segment 330-334 PICK_ATOMS SELECTION_SEGMENT = '331:' '333:', SELECTION_STATUS = 'add' RETURN END_SUBROUTINE ############################################################################## -- Dan Thomas Major (at Dr. B. Fischer's lab) Bar-Ilan University Ramat-Gan, Israel Phone: 972-3-5317785 Fax: 972-3-5348730

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Re: Bad template?--log ali. and top files.
by Lei Wang 02 May '02

02 May '02

log file: ####################################### MODELLER 6v1, 17 Jan 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant 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 master.cl.mssm.edu 2.4.9-13smp i686 Date and time of compilation : 01/24/2002 16:28:15 Job starting time (YY/MM/DD HH:MM:SS): 2002/05/02 11:04:08.230 getprog_531W> ROUTINE redefined: getnames 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 ---------------------------------------------- END OF TABLE ############################################ Top file: ********************************* INCLUDE SET ATOM_FILES_DIRECTORY = './' SET ALNFILE = '1gh0B-3-1eyxK.ali' SET KNOWNS = '1eyxK' SET SEQUENCE = '1gh0B' SET STARTING_MODEL = 1 SET ENDING_MODEL = 5 CALL ROUTINE = 'model' SUBROUTINE ROUTINE = 'getnames' STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION = 'EQ', THEN = ; 'STRING_OPERATE OPERATION = CONCATENATE, STRING_ARGUMENTS = 1gh0B-3-1eyxK .ini, RESULT = MODEL' STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATION = 'EQ', THEN = ; 'STRING_OPERATE OPERATION = CONCATENATE, STRING_ARGUMENTS = 1gh0B-3-1eyxK .rsr, RESULT = CSRFILE' STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = '1gh0B-3-1eyxK' '.sch', RESULT = SCHFILE STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = '1gh0B-3-1eyxK' '.mat', RESULT = MATRIX_FILE SET ROOT_NAME = '1gh0B-3-1eyxK' RETURN END_SUBROUTINE ************************************* >P1;1gh0B structureX:1gh0B: 1 :B: 172 :B:undefined:undefined:-1.00:-1.00 MFDAFTKVVSQADTRGEMLSTAQIDALSQMVAESNKRLDVVNRITSNASTIVSNAARSLFAEQPQLIAPGG-AYT SRRMAACLRDMEIILRYVTYAVFAGDASVLEDRCLNGLRETYLALGTPGSSVAVGVGKMKEAALA---IVNDPAG ITPGDCSALASEIAGYFDRAAAAVS* >P1;1eyxK structureX:1eyxK: 1 : : 164 : :undefined:undefined:-1.00:-1.00 MKSVITTVISAADSAGRFPSSSDLESVQGNIQRASARLEAAEKLASNHEAVVKEAGDACFGKYGYLKNPGEAGEN QEKINKCYRDIDHYMRLVNYSLVIGGTGPLDEWGIAGAREVYRTLNLPTSAYIAAFAFTRDR-LCGPRDMS---- -----AQ-AGVEYSTALDYIINSLS*

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Bad template?
by Lei Wang 02 May '02

02 May '02

1 0

starting with 6v1
by Laurent Troxler 02 May '02

02 May '02

Hi, I am new user of Modeller and as a test I took input files (see bellow) from a friend which were successfully run with version 5. After a few minutes of computing here is the message I get in the logfile: ------------------------------------------------------------------------------------ Initial value of energy before optimization : 15011.7158 Current energy : 14658.3125 Symmetry term within energy : 0.0000 Optimizer exit status : 0 Number of iterations : 67 Number of calls to energy function : 139 Number of updates of dynamic contacts : 8 Number of non-updates of dynamic contacts : 132 Final maximal atomic shift : 0.007 act10___551E> No such routine: recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 17362145 16955.219 16.558 Starting time : 2002/05/02 10:09:43.976 Closing time : 2002/05/02 10:14:02.653 Total CPU time [seconds] : 0.00 ------------------------------------------------------------------------------------ The PDB files come from the PDB server. Is there any problem in the input file ? Thanks for any help or suggestion Laurent ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, @ Laurent TROXLER @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@/\@@/\@@/\@@@@ UPR 9022 CNRS, Réponse Immunitaire et / \/ \/ \ Développement chez les Insectes / /\/ /\/ /\ \ Institut de Biologie Moléculaire et Cellulaire\ \/ /\/ /\/ / 15 rue René Descartes \ \/\ \/\ \/ 67084 Strasbourg Cedex - FRANCE /\ \/\ \/\ \ E-mail: L.Troxler(a)ibmc.u-strasbg.fr / /\/ /\/ /\ \ Tel : (33) 03 88 41 70 07 \ \/ /\/ /\/ / @ Fax : (33) 03 88 60 69 22 @@@@@@@@@@@@@@@@@@@\@@/\@@/\@@/@@@ """"""""""""""""""""""""""""""""""""""""""""""""""\/""\/""\/"""" -- input.top: ------------------------------------------------------------------------------------ INCLUDE #SET OUTPUT_CONTROL = 1 1 1 1 2 SET DIRECTORY = 'model2_dir' SET ATOM_FILES_DIRECTORY = 'model2_dir' SET OUTPUT_DIRECTORY = 'model2_dir' SET PDB_EXT = '.pdb' SET ALNFILE = 'easter2.pir' SET KNOWNS = '1QRZ' '1DST' '1FIW' '1AUT' SET SEQUENCE = 'east' SET MD_LEVEL = 'refine1' SET OUTPUT = 'long' CALL ROUTINE = 'model' ------------------------------------------------------------------------------------ input.pir ------------------------------------------------------------------------------------ >P1;1QRZ structureX:1QRZ : 546:A: 791:A:undefined:undefined:-1.00:-1.00 -----------------------FDCGKPQVE-----------------------PKKCP GRVVGGCV----AHPHSWP-W----------QVSLRTRFG----QHFCGGTLISPEWVLT AAHCLEK---------SPRPSSYKVILGAHQEV--------------------------- ----NL------------EPHVQEIEVS---RLFLEPTR-----------KDIALLKLSS PAVITD------KVIPACLP---SPNYMVA-DRTECFITGWGETQGTFGAG------LLK EAQLPVIENKVCNR--------YEFLNGRVQSTELCAGHL-AGGTDSCQGDSGGPLVCFE KDK----YILQGVTSWG-LGCARPNKPGVYVRVSRFVTWIEGVLR-NN------------ --------------------------* >P1;1DST structureX:1DST : 16: : 243: :undefined:undefined:-1.00:-1.00 ------------------------------------------------------------ --ILGGRE----AEAHARP------------YMASVQLNG----AHLCGGVLVAEQWVLS AAHCLE----------DAADGKVQVLLGAHSLS--------------------------- ----QP------------EPSKRLYDVL---RAVPHPDYQPDTI-----DHDLLLLQLSE KATLGP------AVRPLPWQ---RVDRDVA-PGTLCDVAGWGIVNHAGRRPD-----SLQ HVLLPVLDRATCNR--------RTHHDGAITERLMCAE---SNRRDSCKGDSGGPLVCG- -------GVLEGVVSWGSRVCGNRKKPGIYTRVASYAAWIDSVLA--------------- --------------------------* >P1;1FIW structureX:1FIW : 16:A: 254:A:undefined:undefined:-1.00:-1.00 ------------------------------------------------------------ --IIGGQD----AAHGAWPWM-------VSLQIFTYHNNR---RYHVCGGSLLNSQWLLT AAHCFRI---------KKKVTDWRLIFGAKEVEWG------------------------- --TNKPV-----------KPPLQERYVE---KIIIHEKYSASSE-----ANDIALMKITP PVTCGH------FIGPGCLP---QFRAGPPRVPQTCWVAGWGFLQENARRTSP----MLQ EARVDLIDLGLCNS--------TRWYNGRIRSTNVCAGYP-EGKIDTCQGDSGGPLMCKD SAEN--SYVVVGITSWG-VGCARAKRPGVYTSTWSYLNWIASKIGSTAVHMIQLPT* >P1;1AUT structureX:1AUT : 17:C: 244:C:undefined:undefined:-1.00:-1.00 ------------------------------------------------------------ ---IDGKM----TRRGDSP-W----------QVVLLDSKK----KLACGAVLIHPSWVLT AAHCMD------------ESKKLLVRLGEYDLR--------------------------- ----RW------------EKWELDLDIK---EVFVHPNYSKSTT-----DNDIALLHLAQ PATLSQ------TIVPICLPDSGLAERELNQAGQETLVTGWGYHSSREKEAKRNRTFVLN FIKIPVVPHNECSE----------VMSNMVSENMLCAGIL-GDRQDACEGDSGGPMVASF HG----TWFLVGLVSWG-EGCGLLHNYGVYTKVSRYLDWIHGHIRD-------------- ----------------* >P1;east sequence::::::::0.00: 0.00 ------------------------------------------------------------ ---YGGMK----TKIDEFPWM----------ALIEYTKSQG-KKGHHCGGSLISTRYVIT ASHCVNG------KALPTDWRLSGVRLGEWDT---------------------------- --NTNPDCEVDVRGMKDCAPPHLDVPVE---RTIPHPDYIPASK---NQVNDIALLRLAQ QVEYTD------FVRPICLP-LDVNLRSATFDGITMDVAGWGKTEQLSASN------LKL KAAVEGSRMDECQN-------VYSSQDILLEDTQMCAG-G-KEGVDSCRGDSGGPLIGLD TNKVNTYYFLAGVVSFGPTPCGLAGWPGVYTLVGKYVDWIQNTIES-------------- --------------------------* ------------------------------------------------------------------------------------

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