[phenixbb] negative density for heavy atom?

[Pavel Afonine]

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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