[modeller_usage] Frustrating simple problem!

-- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand Ph +64 3 4797293 Fax +64 3 4797034 >P1;UP_ecoli structureX:1rxc:1 : :253 : :unknown:unknown:-1.00:-1.00 MSKSDVFHLGLTKN------DLQGATLAIVPGDPDRVEKIAALMDKPVKLAS-HREFTTW RAELD------GKPVIVCSTGIGGPSTSIAVEELAQLG------IRTFLRIGTTGAIQPH INVGDVLVTTASVR------LDGASLHFAPLEFPAVADFECTTALVEAAKSIGATTHVGV TASSDTFYPGQERYD-TYSGRVVRHFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAG MVAGVIVNRTQQEIPN--AETMKQTESHAVKIVVEAARRLL* >P1;1uph sequence:uph:1 : :282 : :unknown:unknown:-1.00:-1.00 MKEDILYHFNLTTSRHNFPALFGDVKFVCVGGSPSRMKAFIRCVGAELGLDCPGRDYPNI CAGTDRYAMYKVGPVLSVSHGMGIPSISIMLHELIKLLYYARCSNVTIIRIGTSGGIG-- LEPGTVVITEQAVDTCFKAEFEQIVLGKRVIRKTDLNKKLVQELLLCSAELSEFTTVVGN TMCTLDFYEGQGRLDGALCSYTEKDKQAYLEAAYAAGVRNIEMESSVFAAMCSACGLQAA VVCVTLLNRLEGDQISSPRNVLSEYQQRPQRLVSYFIKKKL* 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, Linux allroy.otago.ac.nz 2.6.5-1.358smp x86_64 Date and time of compilation : 07/16/2002 11:42:16 Job starting time (YY/MM/DD HH:MM:SS): 2004/10/29 16:08:43.499 TOP_________> 106 706 SET ALNFILE = 'UP_human_ecoli' TOP_________> 107 707 SET KNOWNS = '1rxc_mono' TOP_________> 108 708 SET MD_LEVEL = 'refine_3' TOP_________> 109 709 SET SEQUENCE = '1uph' TOP_________> 110 710 SET ATOM_FILES_DIRECTORY = './:../atom_files' TOP_________> 111 711 SET OUTPUT_DIRECTORY = './' TOP_________> 112 712 SET PDB_EXT = '.pdb' TOP_________> 113 713 SET ALIGNMENT_FORMAT = 'PIR' TOP_________> 114 714 SET STARTING_MODEL = 1 TOP_________> 115 715 SET ENDING_MODEL = 5 TOP_________> 116 716 SET DEVIATION = 4.000000 TOP_________> 117 717 SET FINAL_MALIGN3D = 1 TOP_________> 118 718 SET DO_LOOPS = 1 TOP_________> 119 719 SET RADII_FACTOR = 0.915 TOP_________> 120 720 SET LOOP_STARTING_MODEL = 1 TOP_________> 121 721 SET LOOP_ENDING_MODEL = 5 TOP_________> 122 722 SET LOOP_MD_LEVEL = 'refine_2' TOP_________> 123 723 CALL ROUTINE = 'model' TOP_________> 124 399 CALL ROUTINE = 'getnames' TOP_________> 125 509 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 126 510 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 127 511 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 128 512 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 129 513 SET ROOT_NAME = SEQUENCE TOP_________> 130 514 RETURN TOP_________> 131 400 CALL ROUTINE = 'homcsr' TOP_________> 132 106 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 UP_human_ecoli.ali Dynamically allocated memory at amaxbnd [B,kB,MB]: 6262261 6115.489 5.972 openf5__224_> Open 11 OLD SEQUENTIAL UP_human_ecoli.ali read_al_375E> Unknown residue type,position,sequence: 1 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 6262261 6115.489 5.972 Starting time : 2004/10/29 16:08:43.499 Closing time : 2004/10/29 16:08:44.900 Total CPU time [seconds] : 1.38 INCLUDE # remove all the #'d bits. TOP FILE FOR EXTENSIVE REFINEMENT SET INITIAL_MALIGN3D = 1 # don't worry about this. SET OUTPUT_CONTROL = 1 1 1 1 1 # don't worry about this either SET ALNFILE = 'UP_human_ecoli' # alignment file, worry about this SET KNOWNS = '1rxc_mono' # refers to xtal name in algnmnt SET MD_LEVEL = 'refine_3' # sets simulated annealing level 1 high 3 low. 3 good to tansfer coords and fix major gliches. SET SEQUENCE = '1uph' # name of target seq in pir file SET ATOM_FILES_DIRECTORY = './:../atom_files' # for modeller use. It will tell you if it can't find its atoms. SET OUTPUT_DIRECTORY = './' # is exactly that; can alter this SET PDB_EXT = '.pdb' # leave all structures as this SET ALIGNMENT_FORMAT = 'PIR' # leave it this way; easier SET STARTING_MODEL = 1 # these two define the number of SET ENDING_MODEL = 5 # models to build. Unclear why it is this way SET DEVIATION = 4.000000 # defines how much variation is tolerated when building your model from the randomised coords. Leave as is. SET FINAL_MALIGN3D = 1 # don't worry about this SET DO_LOOPS = 1 # for explicit loop building SET RADII_FACTOR = 0.915 # the x factor for good structure. Always include this. SET LOOP_STARTING_MODEL = 1 #back to explicit loop modeling SET LOOP_ENDING_MODEL = 5 # i built 10 per model, 50 loops in total. Too much. 1 model 10 loops SET LOOP_MD_LEVEL = 'refine_2' # md level used; same as above CALL ROUTINE = 'model' # is the modeller key word for modelling building