".. 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
