[phenixbb] negative density for heavy atom?

Kelly Daughtry kddaught at bu.edu
Thu Apr 22 06:38:00 PDT 2010

Hello all,
I have just used phenix autosol and autobuild to phase and build
an initial model of my structure with phase information from Tungsten (W),
collected at the peak wavelength of 1.2134 Angstroms.
Autosol works beautifully! I was able to perform W-SAD and get great maps,
when I initially thought I would have to perform W-MAD!

The problem I am having is during phenix.refine.
When I run the refinement (with and without refining the group anomalous)
and including my experimental phases, I see a giant negative peak in the
Fo-Fc map at the location of my Tungsten. The rest of the map is beautiful.
In the log file, I can tell that the scattering factor is high for tungsten
(see below).

I believe the negative density is telling me I have too many electrons
present at the tungsten site.

Can anyone help me figure out what I am doing wrong?
I have attached my latest log file.

 ----------X-ray scattering dictionary----------

Number of scattering types: 7
  Type Number    sf(0)   Gaussians
   W       1     73.70       2
   Se      1     33.92       2
   S      11     15.96       2
   Mg      1     11.95       2
   O     462      7.97       2
   N     343      6.97       2
   C    1326      5.97       2
  sf(0) = scattering factor at diffraction angle 0.

========================== Anomalous scatterer groups

Anomalous scatterer group:
  Selection: "name W"
  Number of selected scatterers: 1
  f_prime:        16.87
  f_double_prime: 17.72
  refine: f_double_prime

Total number of atoms in anomalous groups: 1

Kelly Daughtry
PhD Candidate
Department of Physiology and Biophysics
Boston University School of Medicine
590 Commonwealth Ave
R 390
Boston MA, 02215
(P) 617-358-5548
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20100422/541b93c0/attachment-0003.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: bt_sad_refine_30.log
Type: application/octet-stream
Size: 67356 bytes
Desc: not available
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20100422/541b93c0/attachment-0003.obj>

More information about the phenixbb mailing list