how to get probe/RINRUS to consider canonical amino acid as SIF "ligand" type

[natedey]

Since probe does not know any information about the seed fragments, it will not attach "ligand" fragment type to seed residues that are canonical amino acids. This doesn't affect normal probe-style model building, but will be totally broke for combinatorial building, and is also causing RINRUS web server problems with the ad hoc "best" model building.

The sif / probe files needs to be further processed to ensure all seed fragments are ligand?

[natedey]

Crap, this is another situation where I can't quickly find an example. Can everyone see if they have a situation where in freq_per_res.dat there are no SIFs that have "ligand"?

[natedey]

Did we resolve this on slack or find any examples?