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Kristof, I don't know of such programs, but it wouldn't surprise me that distang could be jiggered to do what you want. The ribosome folks surely have dealt with this. No matter what program you use (or if you do it "by hand"), let the chemistry guide you: Na+ peaks will be weaker (only 10 electrons; same as water), ~6-coordinate octahedra, coordinated by oxygen atoms, distance ~2.4 A. Coordination (octahedral vs. tetrahedral; not enough hydrogens to make hydrogen bonds) can often distinguish Na+ from water peaks, but sometimes (especially with waters occupying several alternate positions) it can be hard to tell. Cl-, with 18 electrons, will be stronger, often irregular coordination, usually by nitrogens (main chain and Lys/Arg s/c), distance about 3.2-3.4 A. K+ looks like Cl- in terms of peak height, but coord. characteristics are like Na+, but slightly longer distances, slightly less regular geometry. Mg2+ looks like Na+, but distances are ~2.1-2.2 A, and usually very regular octahedral geometry. Ca2+ looks like Mg2+, but slightly longer distances, often expanded (7- or 8-coordinate) coordination shell. Hope this helps, Dave David Borhani, Ph.D. D. E. Shaw Research, LLC 120 West Forty-Fifth Street, 39th Floor New York, NY 10036 [log in to unmask] 212-478-0698 http://www.deshawresearch.com <http://www.deshawresearch.com/> ________________________________ From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Kristof Van Hecke Sent: Thursday, November 06, 2008 7:55 AM To: [log in to unmask] Subject: [ccp4bb] differentiating cation and anions in high resolution structures Dear all, I'm looking for some means (literature references,.. possible programs) to differentiate between cations (Na+), anions (e.g. Cl-) and water molecules in high resolution protein/DNA structures, based on B-factors, distances, coordination, etc.. Does anyone has got an idea of what's the best strategy to follow in these cases..? many thanks Kristof -------------------------------------- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -------------------------------------- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm for more information.