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
Thomas Juettemann wrote: > 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.
http://salilab.org/modeller/9v4/manual/node438.html
> Must the comment line always start with ">P1"?
Yes.
Ben Webb, Modeller Caretaker
Thanks for the quick answer Ben.
I read this page, but it was not clear that the comment line has to start with >P1. It sound to me that there has to be a consistent identifier in the format ">identifier;"
Maybe change the manual entry from: "The line identifier must occur at the beginning of the line." to: "The line identifier ">P1;" must occur at the beginning of the line and must not be changed."
Thanks for the clarification!
Thomas
On Sun, Jun 1, 2008 at 11:26 PM, Modeller Caretaker modeller-care@salilab.org wrote: > Thomas Juettemann wrote: >> >> 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. > > http://salilab.org/modeller/9v4/manual/node438.html > >> Must the comment line always start with ">P1"? > > Yes. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >
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Modeller Caretaker -
Thomas Juettemann