Dear John, many thanks for the reference. Discussions of spatial
autocorrelation measures seem to come up mostly in the econometrics and
geography literature. An expert (I am not ) will no doubt supply better
citations, but the chapters by Haining and Getis in "Handbook of Applied
Spatial Analysis"
http://www.springer.com/economics/regional+science/book/978-3-642-03646-0
may be of use. There is a discussion of testing for white noise with no
spatial dependence in the context of image analysis (courtesy of Peyman
Milanfar ) in section III of
http://www.lx.it.pt/~mtf/Almeida_Figueiredo_TIP2013.pdf
What I was asking about is a fairly simple-minded application of these
tests. Density from calculated structure factors for a 10A cube P1 unit
cell with either O or Na at the center shows clear difference up to 2A
from the peak:
http://diablo.ucsc.edu/~afyfe/navso/navso.pdf
Pearson correlation ignores position and only considers density values.
For distinguishing Na and water amidst the noise of a real map
however, it might (or not..) be helpful to test whether a cluster of
positive/negative values near the peak differs from what can be expected
randomly in the map.
Best,
Alastair Fyfe
On 11/09/2013 11:27 PM, Jrh wrote:
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 <[email protected]> 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: [email protected]
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 <[email protected]
<mailto:[email protected]>> 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
