Hi all, How can I identify atoms like Na+, K+ in the map, from the positive density. 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. Thanks in advance. Subhani
Hi Subhani,
How can I identify atoms like Na+, K+ in the map, from the positive density. 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.
single ions, like Na+ or K+, may not be very easy to distinguish in the map, so you need to do this manually and very carefully, checking the coordination geometry and the maps (both, 2mFo-DFc and mFo-DFc) before and after adding (and subsequent refinement) of ions like this. Then check refined ADPs. You may wan to refine their occupancy. You may want to use phenix.metal_coordination to maintain a reasonable coordination geometry of the ion.
Is there any material I can read on this.
yes, plenty of. Here are a few to start with: 1993(Gregory) 1996(Nayal) 1998(Rulisek) 1999(Harding) 2000(Harding) 2000(Harding) 2001(Pidcock) 2002(Harding) 2002(Mueller) 2002(Thaimattam) 2002(Weiss) 2003(Dudev) 2004(Harding) 2005(Babor) 2005(Sommerhalter) 2006(Dudev) 2006(Harding) 2006(Stefan) 2007(Tamames) 2007(Weiss) 2008(Goyal) 2008(Hsin) 2008(Seebeck) 2008(Zheng_Minor) 2009(Hemavathi) Please let me know if you have any questions or need help with this. Pavel
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
participants (3)
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Nathaniel Echols -
Pavel Afonine -
Subhani Bandara