Dan,
It looks like the program reading in the full sequence, all 3 segments. Try to specify the required segment like e.g.:
MODEL_SEGMENT '1:A' '214:A',
Additionally, it could also happen that there is a problem in the PDB file(unusual residue type or unusual bond distances, atom with empty coordinate entry etc). Switch on full error report for a more detailed error message SET OUTPUT_CONTROL = 1 1 1 1 1
Andras
> ---------------------------------------------------------------------- > > Subject: ALIGN2D problem > Date: Mon, 12 Nov 2001 16:13:19 +0200 > From: Dan Thomas Major majord@mail.biu.ac.il > Organization: Bar-Ilan University > To: modeller_usage modeller_usage@salilab.org > > 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 > >