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 <af...@ucsc.edu> 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: CCP4BB@JISCMAIL.AC.UK >> 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 <ber...@upstate.edu >>> <mailto:ber...@upstate.edu>> 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 >>> >>>
