[modeller_usage] PIR format clarification

["Thomas Juettemann" <>]

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