Hi,
I'm learning how to use modeller (release 6 with linux red hat 9). While CHECK_ALIGNMENT seems accept my alignment, calling the routine 'model' gives me an error when trying to read that same alignment.
I 'm trying to model 41 residues into the first chain of the PDB file 1GL2.pdb (after this 'practice run' I will try to model the four chains of the structure at the same time).
Following are relevant parts of scripts+logs. Any ideas will be greatly appreciated!!!
Javier.
modeller.alignment.ali ---------------------- > >P1;1GL2 > structureX:1GL2:20:A:60:A:Endobrevin:rattus norvegicus:1.9:0.1370 > EGVKNIMTQNVERILARGENLDHLRNKTEDLEATSEHFKTT > * > > >P1;1GGX > sequence:1GGX:1: :41: :ykt6:rattus norvegicus:: > DETKIILHNTMESLLERGEKLDDLVSKSEVLGTQSKAFYKT > *
chech_alignment.top ------------------- > SET OUTPUT_CONTROL = 1 1 1 1 1 > SET ATOM_FILES_DIRECTORY = './../atom_files' > > READ_ALIGNMENT FILE = 'modeller.alignment.ali', ALIGN_CODES = 'all' > WRITE_ALIGNMENT FILE = 'alignment.ali' > CHECK_ALIGNMENT
chech_alignment.log (last part of the file) ------------------- > openf5__224_> Open 11 OLD SEQUENTIAL modeller.alignment.ali > > Read the alignment from file : modeller.alignment.ali > Total number of alignment positions: 41 > > # Code #_Res #_Segm PDB_code Name > ------------------------------------------------------------------------------- > 1 1GL2 A 41 1 1GL2 Endobrevin > 2 1GGX 41 1 1GGX ykt6 > TOP_________> 4 4 WRITE_ALIGNMENT FILE = 'alignment.ali' > > openf5__224_> Open 14 UNKNOWN SEQUENTIAL alignment.ali > TOP_________> 5 5 CHECK_ALIGNMENT > > check_a_343_> >> BEGINNING OF COMMAND > openf5__224_> Open 11 OLD SEQUENTIAL ./../atom_files/1GL2.atm > > check_ali___> Checking the sequence-structure alignment. > > Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: > > ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST > ---------------------------------------------- > END OF TABLE > check_a_344_> << END OF COMMAND > > Dynamically allocated memory at finish [B,kB,MB]: 3061621 2989.864 2.920 > Starting time : 2004/06/08 16:10:06.379 > Closing time : 2004/06/08 16:10:13.541 > Total CPU time [seconds] : 3.47
modelling.top ------------- > INCLUDE > > SET OUTPUT_CONTROL = 1 1 1 1 1 > SET ALNFILE = './alignment.ali' > SET KNOWNS = '1GL2' > SET SEQUENCE = '1GGX' > SET ATOM_FILES_DIRECTORY = '../atom_files' > SET STARTING_MODEL= 1 > SET ENDING_MODEL = 1 > > > CALL ROUTINE = 'model'
modelling.log (last part of the file) ------------- TOP_________> 111 711 CALL ROUTINE = 'model'
TOP_________> 112 399 CALL ROUTINE = 'getnames'
TOP_________> 113 509 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL'
TOP_________> 114 510 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; '
TOP_________> 115 511 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE
TOP_________> 116 512 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE
TOP_________> 117 513 SET ROOT_NAME = SEQUENCE
TOP_________> 118 514 RETURN
TOP_________> 119 400 CALL ROUTINE = 'homcsr'
TOP_________> 120 106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE
Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153.583 2.103 openf5__224_> Open 11 OLD SEQUENTIAL ./alignment.ali
Dynamically allocated memory at amaxbnd [B,kB,MB]: 3061621 2989.864 2.920 openf5__224_> Open 11 OLD SEQUENTIAL ./alignment.ali read_al_375E> Unknown residue type,position,sequence: 1 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]: 3061621 2989.864 2.920 Starting time : 2004/06/08 16:07:55.650 Closing time : 2004/06/08 16:08:04.684 Total CPU time [seconds] : 4.30
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