[phenixbb] negative density for heavy atom?

[Nigel W Moriarty]

Kelly

Another thing you could try, in addition to Pavel's suggestions, is the 
charge on the metal ion.  Tungsten usually has a +6 charge so you can 
tell phenix.refine by adding the charge in column 79-80.

Nigel

12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM   1484  W   W   A   1      31.811  33.879  20.795  0.35 
51.84           W+6


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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>   

-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909     Web   : CCI.LBL.gov

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