trouble with alignment format. tried this :

fubar.fas :
Sorry: Unknown file(s): fubar.fas

fubar.fasta :
Sorry: Wrong alignment format: fubar.fasta

i compared to one that worked yesterday and its not obvious : first
sequence is the target, the pdb sequence is in there (somewhere), i
changed a ">sp" to ">gi"....

The extension ".fas" is not recognized, but ".fasta" should be. My experience with the FASTA parser (for simple sequences, at least) is that it's extremely strict about what is an acceptable format, but that most of the programs/servers that generate/distribute these files are much looser. Could you send me the file (off-list, of course) for debugging?

-Nat