Hi Bing, I think residual density you see is a result of inaccuracy in parameters of Fe, such as coordinates, occupancy or B-factor (or any mixture). This applies to all atoms, but since Fe has more electrons these errors become more readily visible in residual map. Here are a few simulated examples that illustrate the point:
http://cci.lbl.gov/~afonine/tmp/maps.pdf Pavel On Thu, Jun 19, 2014 at 1:44 PM, Wang, Bing <[email protected]> wrote: > 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 >
