Torsten Stauder wrote: > 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 >P1;1rjb structureX:1rjb:572 :A:947 :A:FLT3 wt: : :
or similar.
Ben Webb, Modeller Caretaker