I'm trying to perform ALIGN2D of a target sequence with the sequence of a protein with with X-ray structure, but I keep on getting errors. The protein has several subunits, and I want to align with subunit A only.

The top file is: READ_MODEL FILE = '1HZX.pdb', MODEL_SEGMENT '@:A' 'X:A', OUTPUT_CONTROL = 1 1 1 1 SEQUENCE_TO_ALI ALIGN_CODES = '1HZX' READ_ALIGNMENT FILE = 'hp2y1.seq', ALIGN_CODES = ALIGN_CODES 'hp2y1', ; ADD_SEQUENCE = on READ_TOPOLOGY FILE = '/u/ch/majord/modeller/modeller6a/modlib/top_heav.lib' ALIGN2D WRITE_ALIGNMENT FILE = 'hp2y1-1HZX.ali', ALIGNMENT_FORMAT = 'PIR' WRITE_ALIGNMENT FILE = 'hp2y1-1HZX.pap', ALIGNMENT_FORMAT = 'PAP', ; ALIGNMENT_FEATURES = 'indices helix beta'

The error reported is: ... # Code #_Res #_Segm PDB_code Name -------------------------------------------------------------------------------

1 1HZX 641 3 1HZX undefined 2 hp2y1 373 1 hp2y1 TOP_________> 4 4 READ_TOPOLOGY FILE = '/u/ch/majord/modeller/modeller6a/mo; dlib/top_heav.lib'

openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib//as1.sim.mat rdrrwgh_268_> Number of residue types: 20 dispers_247E> Internal error: 640 641 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1

Dynamically allocated memory at finish [B,kB,MB]: 23066567 22525.945 21.998 Starting time : 2001/11/12 13:53:59.313 Closing time : 2001/11/12 14:41:13.406 Total CPU time [seconds] : 0.00

Thanks, Dan

-- Dan Thomas Major (at Dr. B. Fischer's lab) Bar-Ilan University Ramat-Gan, Israel