hi
this time iam getting a different error
and it says
# Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1hm9 182 1 1hm9 glmu 2 query 165 1 query unknown TOP_________> 121 107 CHECK_ALIGNMENT
check_a_343_> >> BEGINNING OF COMMAND pdbnam__217W> Filename for PDB code not found: 1hm9 Directories: c:/mod6v2/bin/1hm9.atm Extensions : :.atm:.pdb:.ent:.crd rdabrk__288W> Protein not accepted: 1 check_a_337E> Structure not read in: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]: 4967329 4850. 907 4.737 Starting time : 2004/05/03 20:31:36. 970 Closing time : 2004/05/03 20:31:42. 960 Total CPU time [seconds] : 5.99
here is the sequence alignment file
>P1;query sequence:query:1 ::165::unknown:archeae:: SLKVIILAGGRGKRIT--LFKPFLVVCGKPLISWAFDAVNKL-SDKVYTVVGHKAELVEEVLAGQTE IFPTPDISYENDVKYVV------ESLGPPILVLPVDIAFINNNIINNLIERCA--------VDMCTL KSYGSYLGVTYWTGLNFSNYTDIEVK-----EKL-YNINTWEDYIKANKECNIL* >P1;1hm9 structureX:1hm9:2::183::glmu:human:: SNFAIILAAGKGTRMKSDLPKVLHKVAGISMLEHVFRSVGAIQPEKTVTVVGHKAELVEEVLAGQTE -FVTQSEQLGTG-HAVMMTEPILEGLSGHTLVIAGDTPLITGESLKNLIDFHINHKNVATILTAETD NPF-GYGRIVRND--NAEVLRIVEQKDATDFEKQIKEINTGT-YVFDNERLFEA*
and the top file is
INCLUDE # Include the predefined TOP routines
SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'alignmentfile.ali' # alignment filename SET KNOWNS = '1hm9' # codes of the templates SET SEQUENCE = 'query' # code of the target SET ATOM_FILES_DIRECTORY = 'c:/mod6v2/bin/1hm9.atm' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' # do homology modelling
are there any books on learning modeller apartfrom the usual manual
with regards
N.RATHAN KAR
Yahoo! India Matrimony: Find your partner online.