[phenixbb] negative density for heavy atom?

[Kelly Daughtry]

The peak is directly over the WO4 molecule, overlaying pretty well with the
2Fo-Fc density.

In my refinement, I refined the B-factor.
I will try to refine occupancy. That makes sense. If that atom is only there
50% of the time, there would be 50% less contribution, and thus I would see
the negative density.

Thanks for the suggestions!

*******************************************************
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
*******************************************************


On Thu, Apr 22, 2010 at 10:50 AM, Pavel Afonine <PAfonine at lbl.gov> wrote:

>  Hi Kelly,
>
> - where is the peak: at atomic center, near it and looks like a bunch of
> concentric spheres? Then it might be a results of Fourier truncation
> ripples; check this out where I reply to a similar post:
>
> http://proteincrystallography.org/ccp4bb/message14290.html
>
> - did you try to refined f' and f'' of your heavy atom? Actually, I see you
> did (looking at .log file);
>
> - did you try to refine its occupancy and anisotropic ADP?
>
> If you send me (to my email address, not to the whole phenixbb) the data
> and model files, as well as the parameter file and exact command you used, I
> will have a look.
>
> Pavel.
>
>
>
> On 4/22/10 6:38 AM, Kelly Daughtry wrote:
>
> 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
> *******************************************************
>
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>
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