help on using modeller
hi all iam a fresher working on modeller and nothing is going on here properly . i use a win me machine with mod6v2 installed. i tried an alignment file to model but its not working .i have included the top files for reference 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.pdb' # 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
i dont know what does this atom_files mean.plz explain the ERROR it shows is as follows: openf5___224_>open 11 OLD SEQUENTIAL alignmentfile.ali rdpir___376W>not enough fields in the sequence line of the sequence entry:sequence:query:1::165 : : actual fields should be: 7 10 (Fields are separated by a colon. :) read_al_375E>unknown residue type,Position , Sequence: 1 1 recover_____E>ERROR_STATUS=>STOP_ON_ERROR 1 1
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Hi Rathan , The problem lies in your alignment file. Try to verify it with the one given in modeller example. if still cant fix problem. mail your alignment file......without seeing alignment file it's difficult to fix problem,
Yours , B.Nataraj
rathan kar storagerathan@yahoo.co.in wrote: hi all iam a fresher working on modeller and nothing is going on here properly . i use a win me machine with mod6v2 installed. i tried an alignment file to model but its not working .i have included the top files for reference 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.pdb' # 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
i dont know what does this atom_files mean.plz explain the ERROR it shows is as follows: openf5___224_>open 11 OLD SEQUENTIAL alignmentfile.ali rdpir___376W>not enough fields in the sequence line of the sequence entry:sequence:query:1::165 : : actual fields should be: 7 10 (Fields are separated by a colon. :) read_al_375E>unknown residue type,Position , Sequence: 1 1 recover_____E>ERROR_STATUS=>STOP_ON_ERROR 1 1
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B.Nataraj, Final year M.Tech.(Bioinformatics), SASTRA Deemed University, (www.sastra.edu) Thanjavur, Tamil Nadu, India. Email:nataraj@biotech2.sastra.edu Email:natarajmtech@yahoo.co.uk --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now
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
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On Mon, May 03, 2004 at 04:18:52PM +0100, rathan kar wrote: > 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
Given that your alignment specifies 'structureX' for 1hm9, you need to give Modeller a PDB file with the structure in. This needs to be in a file called something like 1hm9.pdb or pdb1hm9.ent.
Ben Webb, Modeller Caretaker
participants (3)
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Modeller Caretaker -
Nataraj Balkrishnan -
rathan kar