[modeller_usage] Errors during generate alignment file for two chains

[jitrayut jitonnom <jitrayut_018 AT hotmail.com>]

Dear modeller users,
 
I have a question on how to generate an alignment of scFv antibody (two chains; light chain and heavy chain). My script is shown below
 
env = environ()
aln = alignment(env) 
mdl = model(env, file='1P4I', model_segment=('FIRST:L','LAST:H'))
aln.append_model(mdl, align_codes='1P4I', atom_files='1P4I.pdb')
aln.append(file='scfv.ali', align_codes='scfv')
aln.align2d()
aln.write(file='scfv-1P4I.ali', alignment_format='PIR')
 
and the PIR file of scfv is 
>P1;scfv
sequence:scfv:1:L:123:H:::0.00: 0.00
vmtqtpalmaaspgekvtitcsvsssisssnlhwyqqksetspkpwiygtsnlasgvpvrfsgsgsgtsysltis
smeaedaatyycqqwsnypltfgagtklelkssggggsggggggssrssl/evkllesggglvkpggslklscaas
gftfssyamswvrqtpekrlewvatissggtytyypdsvkgrftisrdnakntlylqmsslrsedtamyycarfr
ngaywgqgtlvtvsaatttapsv*
 
After i run the script above i found some errros like this;
 
read_al_373E> Protein specified in ALIGN_CODES(i) was not found
              in the alignment file; ALIGN_CODES(       2) =  scfv
 
So, if anyone can help me for this problem i will be appreciated.
 
Jitrayut

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