[phenixbb] ligand fitting

Nathaniel Echols nechols at lbl.gov
Thu Oct 9 10:43:08 PDT 2014

On Thu, Oct 9, 2014 at 10:30 AM, Tim Gruene <tg at shelx.uni-ac.gwdg.de> wrote:

> a CC of 0.49 is quite strong

No no no no no.  This would be true in the general case, but it is
absolutely *not* a good CC for comparing local density, especially when
judging LigandFit results.  A LigandFit CC > 0.8 is almost certainly
correct, > 0.7 is probably correct but may have some misfit atoms or poor
density, > 0.6 is maybe correct but frequently wrong, and < 0.6 is almost
certainly wrong.  For comparing the refined model with 2mFo-DFc density,
the thresholds are higher - a ligand with refined CC < 0.8 should be
treated with extreme suspicion.

Obviously we need a better measure than CC!

> Is there a better way to fit the peptide into density?

LigandFit isn't really the appropriate tool for this - but I don't think
there's actually an easy, automatic way to do what you want in Phenix right
now.  You can run AutoBuild with the existing model defined as "ligands",
but that's going to be very slow.

Although I'm a little surprised that AutoBuild didn't build any peptide -
are you sure it isn't already in your model somewhere?  Or did it build
something and you removed it?  If you didn't include it in the sequence
file, it may be a random set of residues (AutoBuild's guess for the actual

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