Modeller multiple alignment
Hello all, i also tried to run my skript to create a multiple alignment. top-file: READ_MODEL FILE = '1HYZ.pdb', MODEL_SEGMENT 'FIRST:A''LAST:A' SEQUENCE_TO_ALI ALIGN_CODES = '1HYZ' READ_MODEL FILE = '1BIS.pdb', MODEL_SEGMENT 'FIRST:B''LAST:B' SEQUENCE_TO_ALI ALIGN_CODES = '1BIS',ADD_SEQUENCE = on READ_MODEL FILE = '1BIU.pdb', MODEL_SEGMENT 'FIRST:B''LAST:B' SEQUENCE_TO_ALI ALIGN_CODES = '1BIU',ADD_SEQUENCE = on SET ATOM_FILES = '1HYZ' '1BIS' '1BIU' MALIGN3D SET ADD_SEQUENCE = on, ALIGN_BLOCK = NUMB_OF_SEQUENCES READ_ALIGNMENT FILE = 'target.ali', ALIGN_CODES = ALIGN_CODES 'target', ADD_SEQUENCE = on ALIGN2D WRITE_ALIGNMENT FILE='target.ali', ALIGNMENT_FORMAT = 'PIR' WRITE_ALIGNMENT FILE='target.pap', ALIGNMENT_FORMAT = 'PAP' But my job don't terminate.... it always made the same log file log-file: Job starting time (YY/MM/DD HH:MM:SS): 2005/01/13 14:15:56.678 rdactio_534E> Command not recognized: recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 56755 55.425 0.054 Starting time : 2005/01/14 14:15:56.678 Closing time : 2005/01/14 14:15:57.612 Total CPU time [seconds] : 0.90 Please can anybody help me....
Andreas Kowarsch wrote: > i also tried to run my skript to create a multiple alignment. > > top-file: > READ_MODEL FILE = '1HYZ.pdb', MODEL_SEGMENT 'FIRST:A''LAST:A' > SEQUENCE_TO_ALI ALIGN_CODES = '1HYZ' > > READ_MODEL FILE = '1BIS.pdb', MODEL_SEGMENT 'FIRST:B''LAST:B' > SEQUENCE_TO_ALI ALIGN_CODES = '1BIS',ADD_SEQUENCE = on > > READ_MODEL FILE = '1BIU.pdb', MODEL_SEGMENT 'FIRST:B''LAST:B' > SEQUENCE_TO_ALI ALIGN_CODES = '1BIU',ADD_SEQUENCE = on To use SEQUENCE_TO_ALI to add sequence '1BIS' to an alignment, you should use SEQUENCE_TO_ALI ALIGN_CODES = ALIGN_CODES '1BIS',ADD_SEQUENCE = on and similar for 1BIU. Otherwise, you end up with only one sequence in the alignment. > But my job don't terminate.... > it always made the same log file > > log-file: > Job starting time (YY/MM/DD HH:MM:SS): 2005/01/13 14:15:56.678 > > rdactio_534E> Command not recognized: > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 This usually means that your input file has odd line-end characters (e.g. you made it on a Windows box, but are running Modeller on Linux, or vice versa) or that you have tab characters in the file. Check it out in a text editor, and make sure the example files work for you. Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
participants (2)
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Andreas Kowarsch -
Modeller Caretaker