Dear Young-Jin,
If you model it as water, you can use WASP. It's an old program but still accesible here: http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl
Cheers,
Robbie
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> Date: Tue, 2 Aug 2011 14:24:09 -0400
> From: [log in to unmask]
> Subject: [ccp4bb] Sodium ion vs. Water
> To: [log in to unmask]
>
> Dear CCP4 experts,
>
> I would like to ask if there is a clear way to distinguish Na+ and HOH
> molecules in the electron density map. The table I have suggests Na
> to O distance lies between 2.35 and 2.45 that is very hard to discern
> the difference of these two candidates. Na+ may have several
> coordination though (5, 6).
>
> This started from if where the divalent metal locates can be
> substituted by water or sodium. I would appreciate any valuable
> suggestions.
>
> Best,
> Young-Jin
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