[phenixbb] Generating a list of peak heights in a Bijvoet difference Fourier

[John Rose]

Hi again,

I downloaded the latest PHENIX build which has the "Find difference map peaks and holes" option in the GUI.

However, when I run it and look at the anomalous peak heights the peaks do not match the density in the anomalous difference Fourier map created using "Calculate Maps".

To generate the anomalous difference Fourier map I used a SCALEPACK file containing the anomalous pairs and the corresponding refined PDB file with the sulfur atoms omitted.  The data labels used were I(+), sig(+), I(-), sig (-).

The anomalous difference Fourier gave the positions of the missing sulfur as expected.  However, using the same approach (and files) with the "Find difference map peaks and holes" .  The resulting peaks in the GUI or PDB file produced do not correspond to any of the expected sites.




John Rose Ph.D.
Associate Professor
B204B, The Fred C. Davison Life Sciences Complex
120 Green Street
Department of Biochemistry and Molecular Biology
University of Georgia
Athens, GA 30602-7229
=========================================
Phone:     706-542-1750
Fax:        706-542-3077



On Mar 23, 2012, at 3:02 PM, John Rose wrote:

> Hi,
> 
> Is there a way to get a print out of the peak positions and their heights from a Bijvoet difference Fourier map?
> 
> I can generate the map and see the peals but I would like a listing also.
> 
> Thanks,
> 
> John Rose
> 
> 
> John Rose Ph.D.
> Associate Professor
> B204B, The Fred C. Davison Life Sciences Complex
> 120 Green Street
> Department of Biochemistry and Molecular Biology
> University of Georgia
> Athens, GA 30602-7229
> =========================================
> Phone:     706-542-1750
> Fax:        706-542-3077
> 
> 
> 
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> phenixbb at phenix-online.org
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