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] <mailto:[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]
<mailto:[email protected]>] *On Behalf Of *Wang, Bing
*Sent:* Thursday, June 19, 2014 10:44 PM
*To:* [email protected] <mailto:[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
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582
