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

Nathaniel Echols nechols at lbl.gov
Tue Mar 27 09:29:28 PDT 2012


This sounds like a bug.  Could you please send me (off-list) the input
files that you used?

thanks,
Nat

On Tue, Mar 27, 2012 at 9:22 AM, John Rose <rose at bcl4.bmb.uga.edu> wrote:
> 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
>> http://phenix-online.org/mailman/listinfo/phenixbb
>
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