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 > >
