[phenixbb] negative density for heavy atom?

Pavel Afonine PAfonine at lbl.gov
Thu Apr 22 12:15:03 PDT 2010


Hi Kelly,

I think Nigel's suggestion about the charge is very important and may 
explain why you have negative density (due to extra 6 electrons in a 
neutral state). So don't forget to add charge if it's not there yet. 
Refining occupancy may compensate for using incorrect charge, so I would 
ad charge first and if that doesn't help, then refine occupancy (or do 
it at once).

Pavel.


On 4/22/10 11:56 AM, Kelly Daughtry wrote:
> 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 
> <mailto: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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