Re: [modeller_usage] Tyrosinekinase-Modelling

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
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