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
>
>
|