A small problem with the align2d script from the TvLDH tutorial examples. The align2d.top script is as follows:
READ_MODEL FILE = '4mdh.pdb' SEQUENCE_TO_ALI ALIGN_CODES = '4mdhA' READ_ALIGNMENT FILE = 'TvLDH.ali', ALIGN_CODES = ALIGN_CODES 'TvLDH', ADD_SEQUENCE = on ALIGN2D WRITE_ALIGNMENT FILE='TvLDH-4mdhA.ali', ALIGNMENT_FORMAT = 'PIR' WRITE_ALIGNMENT FILE='TvLDH-4mdhA.pap', ALIGNMENT_FORMAT = 'PAP'
Running this produced the following warnings in the align2d.log file :
iatmcls_286W> MODEL atom not classified: ALA:OT1 ALA iatmcls_286W> MODEL atom not classified: ALA:OT2 ALA pdbnam__217W> Filename for PDB code not found: 4mdhA Directories: ./ Extensions : :.atm:.pdb:.ent:.crd rdabrk__288W> Protein not accepted: 1 mkapsa__293W> No TOPOLOGY_LIB is in memory. Use READ_TOPOLOGY to read one.
This seems to indicate that the template file or template sequence cannot be found. However, the alignment goes ahead and is fine (ie. both target and template sequences were present). Could someone please explain.
As usual, I'm running MODELLER 6v2 on Mac OS/X Darwin.