A related question on this topic: calculated density curves drop off at
different rates even for isoelectronic ions/water. Thus the neighborhood
of a mismodeled peak in the error map would be expected to show
detectable, non-random, spatial dependence. On the other hand the
neighborhood of a well-modeled peak should be indistinguishable from
white noise. Though there are statistics (Moran's I, Geary's C ) for
testing spatial effects in variable correlation that could be applied
to DFc/ 2mFo-DFc correlation, I haven't seen them applied to this
problem. Can anyone suggest a relevant reference? This seems a useful
adjunct to bond-valence/non-bonding contact methods.
thanks,
Alastair Fyfe
On 11/09/2013 03:24 AM, Robbie Joosten wrote:
> Hi Ed,
>
> WHAT_CHECK checks water that may be ions and also checks the identity of ions already built. The check my metal server is also very good for final validation of ions.
>
> Cheers,
> Robbie
>
> Sent from my Windows Phone
> ________________________________
> Van: Edward A. Berry
> Verzonden: 9-11-2013 7:29
> Aan: [log in to unmask]
> Onderwerp: Re: [ccp4bb] monovalent cation binding sites
>
> Thanks, all!
> Ed
>
>
> Nat Echols wrote:
>> In the latest Phenix:
>>
>> mmtbx.water_screen model.pdb data.mtz elements=NA,K
>>
>> The data are required right now, but I could be convinced to make that optional.
>>
>> -Nat
> Diana Tomchick wrote:
>> There's a command in coot that identifies "waters" that have an unusually high coordination number. You then need to manually inspect the electron density map and bond lengths, atom type, etc.
>>
>> Diana
> Shekhar Mande wrote:
>> Ed, I dont about monovalent metals (they are typically liganded by hydroxyls of Ser/Thr,
>> or the main chain carbonyls). But we did an analysis of divalent metals in proteins, and
>> found several instances, where crystallographers might have mistaken a metal to be a
>> water. Thus, in the PDB, what is reported to be a water, might actually turn out to be a
>> metal! Some of our sites have used to predict functions of proteins, where enzyme assays
>> required addition of metals, and hence, I am gratified that it is useful! I am enclosing
>> a PDF with this.
>>
>> We also have a server.
>>
>> Shekhar
> Dunten, Pete W. wrote:
>> Ed, O had a command
>> that scrutinized waters
>> and helped find metals
>> modeled as water.
>>
>> Victor Lamzin has a program
>> whose name I'be momentarily
>> forgotten which gives plots of
>> e-density at atomic centers
>> versus B-factor, for each atom
>> type. Points off the lines are
>> candidates for incorrectly
>> modeled metals.
>>
>> Pete
> Dunten, Pete W. wrote:
>> See attached and the reference noted therein.
>>
>> Best wishes, Pete
>> ________________________________________
>
> Parthasarathy Sampathkumar wrote:
>> Hi Ed,
>>
>> WASP analyse water molecules in high-resolution protein structure to check if some of
>> those could be metal ions. WASP could be run as a part of STAN server.
>> STAN - the STructure ANalysis server from USF (
>> http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl )
>>
>> One could also identity potential metal ions within COOT as well.
>>
>> HTH,
>> Best Wishes,
>> Partha
>>
>>
>>
>>
>> On Fri, Nov 8, 2013 at 9:09 PM, Edward A. Berry <[log in to unmask]
>> <mailto:[log in to unmask]>> wrote:
>>
>> Is there a server or program to predict binding sites for monovalent metal ions?
>> Ideally should work with just the protein structure, but a program that sorts through
>> the waters in a high resolution structure and tells which are likely to be K+ or Na+
>> would also be of interest.
>>
>> Ed
>>
>>
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