Well - I am not familiar with the PHENIX dictionary but you are right; if you restrain metal bond distances the structure will reflect the restraints but if you don't restrain the distances then the respective gradients for a light atom and a heavy one can produce some very odd and unrealistic results in the refined coordinates. I prefer to assign restraints and give an SD for that distance but it is hard to know what has happened with any set of coordinates you download. And then the data base searches find a set of "experimental" distances which are not in fact experimental at all. Eleanor
On 24 May 2012 18:58, Ivan Shabalin <shabali...@inbox.ru> wrote: > Dear all, > > I found that thread in my search of what ideal values for metal Phenix is > using. I tried to use that command "phenix.pdb_interpretation model.pdb > write_geo_files=true" for my pdb file, and I get all the values for most > atoms, like: > > >>bond pdb=" CB LEU B 332 " segid="B " > pdb=" CG LEU B 332 " segid="B " > ideal model delta sigma weight residual > 1.530 1.511 0.019 2.00e-02 2.50e+03 9.40e-01 > >> > > but for Mg ions i did not find the ideal value: > >> > nonbonded pdb=" O HOH C 405 " > pdb="MG MG M 1 " > model vdw > 1.906 3.250 > >> > > Can I specify some keywords to get it also for Mg? > > I looked through phenix folders and I found energy_lib.cif file. There are > the following records for Mg: > > MG NPA metal 500.000 2.090 . > MG NPB metal 500.000 2.090 . > MG OHA metal 500.000 2.150 . # ? > MG OHB metal 500.000 2.150 . # ? > MG OHC metal 500.000 2.150 . # ? > MG O metal 500.000 2.180 . # ? > > Do I understand correctly, that these are actually the default values? If > I use Phenix with default parameters, then distances will tend to become > ideal? Especially at low resolution when X-ray weight is low? > And what does mean, that for Mg there is no standard deviation of the > bonds (. # ? is placed instead)? How phenix will handle it? will it assign > some default esd? > > I appreciate any comments! Thanks a lot!! > > > With best regards, > > Ivan Shabalin, Ph.D. > Research Associate at Minor Lab, University of Virginia > 4-224 Jordan Hall, 1340 Jefferson Park Ave. > Charlottesville, VA 22908 >
