Dhananjay wrote: > Part of model-default.log file is as follows: > > Read the alignment from file : alignment.ali > Total number of alignment positions: 610 > > # Code #_Res #_Segm PDB_code Name > ------------------------------------------------------------------------------- > 1 1g7s 594 1 1g7s Initiation factop > 2 NIF 595 1 NIF > runcmd______> alignment.check () > > check_a_343_> >> BEGINNING OF COMMAND > openf5__224_> Open 11 OLD SEQUENTIAL 1g7s > rdpdb___303E> No atoms were read from the specified input PDB file, > since the > starting residue number and/or chain id in MODEL_SEGMENT (or > the alignment file header) was not found; > requested starting position: residue number " 1", chain " A" > rdabrk__288W> Protein not accepted: 1 1g7s > check_a_337E> Structure not read in (please consult the log file > for more details): 1 1g7s
Check the 1g7s PDB file. Like the log file says, it didn't read in the sequence because your alignment says to start from residue 1 in chain A, and it couldn't find that in the PDB file.
Ben Webb, Modeller Caretaker