[ccp4bb] monovalent cation binding sites

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

Re: [ccp4bb] monovalent cation binding sites

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 potenti

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

Re: [ccp4bb] monovalent cation binding sites

Dear Ed, I imagine this reference:- http://dx.doi.org/10.1021/ja908703c Will be of interest. 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/i

Re: [ccp4bb] monovalent cation binding sites

: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 >

Re: [ccp4bb] monovalent cation binding sites

er 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:

Re: [ccp4bb] monovalent cation binding sites

ilt. 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: CCP4B

Re: [ccp4bb] monovalent cation binding sites

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 Ph