Hi, again.
Thanks to all those who answered my previous questions. I haven't had time to checkout the SEQUENCE_SEARCH suggestion, but if MODELLER takes 2 hours or more to find a suitable template, perhaps a BLAST search of the PDB or ExPDB databases would be quicker.
Also, the MODELLER ftp server is up and running, and I have downloaded and looked at some of the files. In particular, I have downloaded the structure files associated with the TvLDH example.
This leads me on to my next problem - I have downloaded the file 'compare.top' and the structure files 1bmdA.pdb, 4mdhA.pdb, 5mdhA.pdb and 7mdhA.pdb, along with TvLDH.ali. Running the 'compare.top' script produced the following (edited) .log file:
Multiple dynamic programming alignment (MALIGN): Residue-residue metric : ${MODINSTALL6v2}/modlib//as1.sim.mat ALIGN_BLOCK : 1 Gap introduction penalty: -900.0000 Gap extension penalty : -50.0000 Length of alignment : 355 pdbnam__217W> Filename for PDB code not found: 1bmd Directories: ./ Extensions : :.atm:.pdb:.ent:.crd rdabrk__288W> Protein not accepted: 1 pdbnam__217W> Filename for PDB code not found: 4mdh Directories: ./ Extensions : :.atm:.pdb:.ent:.crd rdabrk__288W> Protein not accepted: 2 pdbnam__217W> Filename for PDB code not found: 5mdh Directories: ./ Extensions : :.atm:.pdb:.ent:.crd rdabrk__288W> Protein not accepted: 3 pdbnam__217W> Filename for PDB code not found: 7mdh Directories: ./ Extensions : :.atm:.pdb:.ent:.crd rdabrk__288W> Protein not accepted: 4 fndatmi_284E> Beginning atom index for a residue out of bounds: 0 0 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]: 14267969 13933.563 13.607 Starting time : 2002/09/24 11:50:17.110 Closing time : 2002/09/24 11:50:45.289 Total CPU time [seconds] : 12.99
I edited the compare.top file, putting an INCLUDE command as the first line. This produced the following (again, edited) .log file:
Multiple dynamic programming alignment (MALIGN): Residue-residue metric : ${MODINSTALL6v2}/modlib//as1.sim.mat ALIGN_BLOCK : 1 Gap introduction penalty: -900.0000 Gap extension penalty : -50.0000 Length of alignment : 355 fndatmi_284E> Beginning atom index for a residue out of bounds: 0 0 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]: 14267969 13933.563 13.607 Starting time : 2002/09/24 11:53:44.067 Closing time : 2002/09/24 11:53:59.605 Total CPU time [seconds] : 13.67
Could someone please where the error is, and why, initially, the .pdb files are not seen.
I am running MODELLER on Mac OSX (Powerbook G4).
Thanks,
Alex.