Hi Bernhard, the attached PDF displays data from Phil Coppens' web site. The difference is really small and if you take the B-value into account, there are much greater errors that prevent you from noticing this difference.
I spent a few months on Cromer-Mann-Parameters about a year ago, and as usual, it was a frustrating (albeit very educational) exercise trying to beat shelxl ;-) Cheers, Tim On 06/20/2014 01:14 PM, Bernhard Rupp wrote: > Thanks, Pavel, George. > > I think the difference is indeed marginal for the scattering function except > for > > the part close to f000, which may be the major reason why it works fine with > the atoms. > > But in principle there is nothing that prevents us from using the correct > Cromer-Mann > > coefficients for the ions by interpreting an atom record eg. Fe2+ as the > appropriate ion- > > although our scattering functions despite being ideal seem good enough for at > least standard > > refinement. > > I cannot find a figure right now but ‘ll plot a few graphs of atom vs ion > scattering functions > > from C-Ms when I get to it… > > > > Thx, BR > > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of George > Sheldrick > Sent: Friday, June 20, 2014 9:41 AM > To: [email protected] > Subject: Re: [ccp4bb] refine an ion atom with different status > > > > I agree with Pavel. Even for accurate small molecule data with R-values below > 3% the differences are hardly significant, the 'B-factors' compensate so > well. The large majority of small molecule structures are refined with > neutral atom scattering factors even if ions are present. The calculated > scattering factor for an isolated ion in the gas phase is not really > appropriate for the environement of an ion in the crystal anyway. > > George > > > On 06/20/2014 07:18 AM, Pavel Afonine wrote: > > Hi Bernhard, > > > > phenix.refine makes use of charge if specified in PDB file (rightmost column > after the chemical element type) to use appropriate form-factors. However, > occupancies and B-factors are very efficient mops to accommodate a broad > range of discrepancies between model and reality. So whether the effect of > using charge is going to be noticeable, I guess, depends on the data quality > (resolution, completeness, etc) and how strong the effect itself is. > > > > Also, it should be relatively easy to make a numerical experiment with > calculated data to see how the total scattering brakes down into individual > contributions. > > > > Pavel > > > > On Thu, Jun 19, 2014 at 6:42 PM, Bernhard Rupp <[email protected]> > wrote: > > “.. change the valence of ion or metal except by changing the occupancy” > > > > Changing the occupancy is entirely different from changing valence. The > former scales the scattering function proportionally, while the elimination > of outer shell electrons predominantly reduces the very low resolution part > (starting at f000) of the scattering function. Verifying the correct > scattering function (e.g. Fe+++ vs Fe++ vs Fe atomic) used by the refinement > program could be useful. I am curious: Garib, Pavel, Busters: How is that > currently implemented? > > > > Best, BR > > > > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Wang, > Bing > Sent: Thursday, June 19, 2014 10:44 PM > To: [email protected] > Subject: [ccp4bb] refine an ion atom with different status > > > > Hi CCP4 guys, > > I have a structure with heme containing an ion atom in it. Except the 4 > coordinated nitrogen atoms in the heme, this ion also coordinates with one > histidine residue and one ligand. But I found two negative red balls (top one > and bottom one) around the ion, which is perpendicular to the heme plate and > keeping in the same line with the histidine and my ligand (See the figure > Ion_100 from coot in the attachment). I guess this ion has different status > in it (e. g. mixture of Fe2+ and Fe3+). I simply tried the lower occupancy of > ion. It clearly eliminate the negative ball at the bottom and most of the > negative balls at the top, but also produced one more positive peak with > slight movement instead of the negative ball at the bottom (See the figures > Ion_90, Ion_85, Ion_80). The numbers in the image name represents the > different occupancy ("100" means 100%, "80" means 80%). > > So any suggestions to solve this problem? Except changing the occupancy, is > there a more precise way to change the valence of ion or metal in coot, and > then refine in Refmac or Phenix? > > Thanks! > > Bing > > > > > > > > -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Fe2+.pdf
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