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
