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 >
