Read the alignment from file : alignment_final.ali
Total number of alignment positions: 426
# Code #_Res #_Segm PDB_code Name
-------------------------------------------------------------------------------
1 a627 426 1 a627 FLT3 mutated ITD
2 1rjb 344 1 1rjb FLT3 wild type
runcmd______> alignment.check()
check_a_343_> >> BEGINNING OF COMMAND
check_a_337E> Structure not read in (please consult the log file
for more details): 1 a627
When I run your input files with mod8v2, my log file says:
runcmd______> alignment.check()
check_a_343_> >> BEGINNING OF COMMAND
openf5__224_> Open 11 OLD SEQUENTIAL ./pdb1rjb.ent
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 " 572", chain " "
rdabrk__288W> Protein not accepted: 1 1rjb
check_a_337E> Structure not read in (please consult the log file
for more details): 1 1rjb
I don't know why you're not seeing this in your own log file. But what
this error means is that alignment is telling Modeller to read from
residue number 572 in the ' ' chain (i.e. no ID). But the first chain in
1rjb is the 'A' chain. So you need to modify your alignment file header
to read