On Tue, Feb 28, 2012 at 9:54 AM, Subhani Bandara
How can I identify atoms like Na+, K+ in the map, from the positive density.
Add as many "waters" as possible, refine, then run this in the nightly build: mmtbx.find_peaks_holes data.mtz model.pdb write_pdb=True It will output a PDB file containing large positive peaks - most importantly, chain D will be waters with positive mFo-DFc density after refinement, which means they're something heavier. (This will be phenix.find_peaks_holes starting with the next build, and there is also a GUI but it's not finished yet.)
Also can I add solvents like MPD and Tris buffer if any. Is there a specific way or do I have to run ligand fit. Is there any material I can read on this.
LigandFit might work - these are fairly small ligands though, so I'm not sure what will happen. -Nat