Dear Alastair,
This reference:-
http://dx.doi.org/10.1107/S0907444903004219
seems related to your email input below.
I would be grateful though to be guided with a couple of references from you on the topics you raise.
Thankyou in anticipation,
Best wishes,
John
Prof John R Helliwell DSc FInstP CPhys FRSC CChem F Soc Biol.
Chair School of Chemistry, University of Manchester, Athena Swan Team.
http://www.chemistry.manchester.ac.uk/aboutus/athena/index.html
On 9 Nov 2013, at 20:30, Alastair Fyfe <[log in to unmask]> wrote:
> 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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