there is no "sequenceX" entry type in the alignment, csak "sequence" or "structureX"

Andras

> Á¶º´°ü wrote: > > Hi modellers.. > > Today, i met this message from modeller....but i can not understand > why this occurs.... > i retrived 3TAT.pdb file from www.pdb.org and prepared ate1.ali file > from ClustalW in PIR format... > The related files and log file are below.... > why modeller give me the 'sequence not read in' message?? > > Byung-Kwan > > - ate1.ali file > >P1;ate1 > sequence:ate1:1: :397: :ArATEs:Enterobacter_sp: : > MFQKVDAYAGDPILSLMER.....QRVAQAFAAVM* > >P1;3TAT > sequenceX:3TAT: :A: :A:ArATEc:Escherichia_coli: : > MFQKVDAYAGDPILTLMER.....QRVAKAFAAVM* > > - 3TAT.pdb > > - ate1.top > # Homology modelling by the MODELLER TOP > > INCLUDE > > SET OUTPUT_CONTROL = 1 1 1 1 1 > SET ALNFILE = 'ate1.ali' > SET KNOWNS = '3TAT' > SET SEQUENCE = 'ate1' > SET ATOM_FILES_DIRECTORY = > '/usr/bin/modeller6v1/examples/tutorial-model/atm/' > SET STARTING_MODEL= 1 > SET ENDING_MODEL= 5 > SET RAND_SEED = '76077' > SET MD_LEVEL = 'refine1' > > > CALL ROUTINE = 'model' > - ate1.log > > 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 localhost 2.2.18-10 > i686 > Date and time of compilation : 01/24/2002 16:28:15 > Job starting time (YY/MM/DD HH:MM:SS): 2002/09/03 13:59:14.415 > > TOP_________> 105 705 SET ALNFILE = 'ate1.ali' > > TOP_________> 106 706 SET KNOWNS = '3TAT' > > TOP_________> 107 707 SET SEQUENCE = 'ate1' > > TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = './:' > > TOP_________> 109 709 SET STARTING_MODEL = 1 > > TOP_________> 110 710 SET ENDING_MODEL = 5 > > TOP_________> 111 711 SET RAND_SEED = '76077' > > TOP_________> 112 712 SET MD_LEVEL = 'refine1' > > TOP_________> 113 713 CALL ROUTINE = 'model' > > TOP_________> 114 398 CALL ROUTINE = 'getnames' > > TOP_________> 115 508 STRING_IF STRING_ARGUMENTS = MODEL > 'undefined', OPERATION; > = 'EQ', THEN = 'STRING_OPERATE OPERATION = > CONCATENA; > TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = > MODEL' > > TOP_________> 116 509 STRING_IF STRING_ARGUMENTS = CSRFILE > 'undefined', OPERATI; > ON = 'EQ', THEN = 'STRING_OPERATE OPERATION > = CONCATE; > NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT > = CSRFILE; > ' > > TOP_________> 117 510 STRING_OPERATE OPERATION = > 'CONCATENATE', ; > STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = > SCHFILE > > TOP_________> 118 511 STRING_OPERATE OPERATION = > 'CONCATENATE', ; > STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = > MATRIX_FI; > LE > > TOP_________> 119 512 SET ROOT_NAME = SEQUENCE > > TOP_________> 120 513 RETURN > > TOP_________> 121 399 CALL ROUTINE = 'homcsr' > > TOP_________> 122 106 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 ate1.ali > > Dynamically allocated memory at amaxbnd [B,kB,MB]: > 7974421 7787.521 7.605 > openf5__224_> Open 11 OLD SEQUENTIAL ate1.ali > > Read the alignment from file : ate1.ali > Total number of alignment positions: 397 > > # Code #_Res #_Segm PDB_code Name > ------------------------------------------------------------------------------- > 1 3TAT 397 1 3TAT ArATEc > 2 ate1 397 1 ate1 ArATEs > TOP_________> 123 107 CHECK_ALIGNMENT > > check_a_343_> >> BEGINNING OF COMMAND > 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]: > 7974421 7787.521 7.605 > Starting time : 2002/09/03 > 13:59:14.415 > Closing time : 2002/09/03 > 13:59:15.159 > Total CPU time [seconds] : 0.70