Pred2ary Known Problems and Bugs

I assume you have the program working, or you wouldn't be seeing this help file. Possible problems with starting the program are described on the web page: http://www.cmpharm.ucsf.edu/~jmc/pred2ary/problems.html.

I tried loading a file containing an amino acid sequence, but Pred2ary says "no proteins found"

Try putting in a line with a ">" symbol followed by the name of the protein before the amino acid sequence. This is required for recognition of a sequence in FASTA format. See formats for more info.

I tried loading in a MSF file, but Pred2ary says "no proteins found"

To be properly recognised, the MSF file must start with a line beginning with "MSF " followed by the name of the protein, or else it can start with the characters "!!AA_MULTIPLE_ALIGNMENT". See formats for more info.

I tried printing, and got a window saying "could not execute print command".

This is a bug in SGI java, and possibly other unix systems also. Try printing to a file, then sending that file to the printer yourself with "lp" or "lpr".