On Thu, Oct 9, 2014 at 1:16 PM, Sneha Rangarajan <rsneha@umd.edu> wrote:
@Nat: If I want to run autobuild to fit the ligand into the density, should I give it my “apo” model as ‘starting model’ and peptide.pdb as ‘ligands’ alongwith
the mtz?
No, in AutoBuild terminology, "ligands" means "atoms I want AutoBuild to leave alone (but include in refinement)", which would mean your apo model. You wouldn't supply peptide.pdb at all, because AutoBuild isn't going to move it into the correct place; ideally you want it to just build new residues into the appropriate density.
To be honest I think I would be tempted to simply build the peptide by hand, which shouldn't be too difficult at this resolution. I'm normally a big fan of letting the program do all of the heavy lifting, but this is one of those corner cases where the manual approach might be more efficient. (This is a point for future improvement in Phenix, of course.) Your own opinion of how easy it will be may be different than mine, however.