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----- Forwarded message from Dong Chen dong.chen@usu.edu -----
Subject: Help for "Sequence difference between alignment and pdb" Date: Fri, 26 Sep 2003 18:10:45 -0600 From: "Dong Chen" dong.chen@usu.edu To: modeller-care@salilab.org
Hi,
I am trying to model a protein by its own structural information, but it gives me "Sequence difference between alignment and pdb" error message in the log.file. Could somebody help to see where is problem. Attached are the files I used.
Thanks,
Dong
####1EDU.atm ####model-Peter.top: # Homology modelling by the MODELLER TOP routine 'model'.
INCLUDE # Include the predefined TOP routines
SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'alignment_Peter.ali' # alignment filename SET KNOWNS = '1EDU' # codes of the templates SET SEQUENCE = 'peter' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate)
CALL ROUTINE = 'model' # do homology modelling
####alignment_Peter.ali: C; A sample alignment in the PIR format; used in tutorial >P1;1EDU structure:1EDU:2:A :150:A: : : : -NIVHNYSEAEIKVREATSNDPWGPSSSLXSEIADLTYNVVAFSEIXSXIWKRLNDHGKNWRHVY KAXTLXEYLIKTGSERVSQQCKENXYAVQTLKDFQYVDRDGKDQGVNVREKAKQLVALLRDEDR LREERAHALKTKEKLAQTATA* >P1;peter sequence:peter:1 : :150 : : : : : -NIVHNYSEAEIKVREATSNDPWGPSSSLXSEIADLTYNVVAFSEIXSXIWKRLNDHGKNWRHVY KAXTLXEYLIKTGSERVSQQCKENXYAVQTLKDFQYVDRDGKDQGVNVREKAKQLVALLRDEDR LREERAHALKTKEKLAQTATA*
####logfile.log:
MODELLER 6v2, 17 Feb 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, Windows_NT BTC101DC x86 Family 15 Model 1 Stepping 2, Genuin Date and time of compilation : Jul 09 2002 16:21:30 Job starting time (YY/MM/DD HH:MM:SS): 2003/09/23 17:56:59.346
TOP_________> 105 705 SET ALNFILE = 'alignment_Peter.ali'
TOP_________> 106 706 SET KNOWNS = '1EDU'
TOP_________> 107 707 SET SEQUENCE = 'peter'
TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = './:../atom_files'
TOP_________> 109 709 SET STARTING_MODEL = 1
TOP_________> 110 710 SET ENDING_MODEL = 1
TOP_________> 111 711 CALL ROUTINE = 'model'
TOP_________> 112 399 CALL ROUTINE = 'getnames'
TOP_________> 113 509 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL'
TOP_________> 114 510 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; '
TOP_________> 115 511 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE
TOP_________> 116 512 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE
TOP_________> 117 513 SET ROOT_NAME = SEQUENCE
TOP_________> 118 514 RETURN
TOP_________> 119 400 CALL ROUTINE = 'homcsr'
TOP_________> 120 106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE
Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153.583 2.103 openf5__224_> Open 11 OLD SEQUENTIAL alignment_Peter.ali
Dynamically allocated memory at amaxbnd [B,kB,MB]: 4458129 4353.642 4.252 openf5__224_> Open 11 OLD SEQUENTIAL alignment_Peter.ali read_al_374_> Non-standard residue type,position,sequence: X 29 1 read_al_374_> Non-standard residue type,position,sequence: X 46 1 read_al_374_> Non-standard residue type,position,sequence: X 48 1 read_al_374_> Non-standard residue type,position,sequence: X 67 1 read_al_374_> Non-standard residue type,position,sequence: X 70 1 read_al_374_> Non-standard residue type,position,sequence: X 89 1 read_al_374_> Non-standard residue type,position,sequence: X 29 2 read_al_374_> Non-standard residue type,position,sequence: X 46 2 read_al_374_> Non-standard residue type,position,sequence: X 48 2 read_al_374_> Non-standard residue type,position,sequence: X 67 2 read_al_374_> Non-standard residue type,position,sequence: X 70 2 read_al_374_> Non-standard residue type,position,sequence: X 89 2
Read the alignment from file : alignment_Peter.ali Total number of alignment positions: 149
# Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1EDU 149 1 1EDU 2 peter 149 1 peter TOP_________> 121 107 CHECK_ALIGNMENT
check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files/1EDU.atm rdabrk__291E> Sequence difference between alignment and pdb :
STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 1 29 24 UNK 11 MET PSSSLXSEIAD rdabrk__288W> Protein not accepted: 1 check_a_337E> Structure not read in: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]: 4458129 4353.642 4.252 Starting time : 2003/09/23 17:56:59.346 Closing time : 2003/09/23 17:57:01.549 Total CPU time [seconds] : 1.72
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