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
