Hello, Thanks a lot to Bozidar and Andras who kindly answered my question about 'memory requirements'. I have checked my parameters that seem to be big enough and I decided to have a look at things from the beginning, installing the recent modeller6v1.

I still get a segmentation fault executing the tutorial examples (initial.top and model-defailt.top) with mod6v1_iris4d on my SGI Octane workstation ('trace' enclosed). Could you please tell me on which Silicon Graphics machine (which OS version) was modeller6 compiled? I would be grateful for any help. All the best, Ada ------------------------------------------------------------------------- balthus:adap 18>/ext5/usr/local/bin/modeller6v1/bin/mod6v1_iris4d initial

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, IRIX64 balthus 6.5 IP30 Date and time of compilation : 01/25/2002 20:36:35 Job starting time (YY/MM/DD HH:MM:SS): 2002/01/30 19:25:47.221

TOP_________> 2 2 READ_ALIGNMENT ALIGNMENT_FORMAT = 'PIR', FILE = 'alignmen; t.ali'

openf5__224_> Open 11 OLD SEQUENTIAL alignment.ali openf5__224_> Open 11 OLD SEQUENTIAL alignment.ali

Read the alignment from file : alignment.ali Total number of alignment positions: 106

# Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 5fd1 106 1 5fd1 ferredoxin 2 1fdx 54 1 1fdx ferredoxin TOP_________> 3 3 ID_TABLE MATRIX_FILE = 'id.mat'

Segmentation fault ----------------------------------------------------------------------- and the second one: balthus:adap 29>$MODINSTALL6v1/bin/mod6v1_iris4d model-default

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, IRIX64 balthus 6.5 IP30 Date and time of compilation : 01/25/2002 20:36:35 Job starting time (YY/MM/DD HH:MM:SS): 2002/01/30 19:55:04.865

TOP_________> 105 705 SET ALNFILE = 'alignment.ali'

TOP_________> 106 706 SET KNOWNS = '5fd1'

TOP_________> 107 707 SET SEQUENCE = '1fdx'

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_________> 112 398 CALL ROUTINE = 'getnames'

TOP_________> 113 508 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL'

TOP_________> 114 509 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; '

TOP_________> 115 510 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE

TOP_________> 116 511 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE

TOP_________> 117 512 SET ROOT_NAME = SEQUENCE

TOP_________> 118 513 RETURN

TOP_________> 119 399 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.ali

Dynamically allocated memory at amaxbnd [B,kB,MB]: 3882961 3791.954 3.703 openf5__224_> Open 11 OLD SEQUENTIAL alignment.ali

Read the alignment from file : alignment.ali Total number of alignment positions: 106

# Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 5fd1 106 1 5fd1 ferredoxin 2 1fdx 54 1 1fdx ferredoxin TOP_________> 121 107 CHECK_ALIGNMENT

check_a_343_> >> BEGINNING OF COMMAND Segmentation fault ========================================================================