Dear all,
a question about the PIR format in the align input file. I could not find the answer in the manual or the archives, apologies if I overead it.
I created some PIR alignments with comment lines like these (2 different files):
>cdk-cyclin;1W98.core >CDK2HUMANaCGA2HUMAN;1FIN
both times MODELLER crashed and I got these error messages:
read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 1W98.core
read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 1FIN.core
changing the comment lines to: >P1;1W98.core >P1;1FIN
solved the problem.
Must the comment line always start with ">P1"? If not, what are the limitations length and/or alphabet-wise?
Many thanks, Thomas