Generating a list of peak heights in a Bijvoet difference Fourier
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
On Fri, Mar 23, 2012 at 12:02 PM, John Rose
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.
Download the latest nightly build and run this command (or use the GUI): phenix.find_peaks_holes data.mtz model.pdb You may also need to specify this to make sure it uses the anomalous data: xray_data.labels="F(+),SIGF(+),F(-),SIGF(-)" (the command is supposed to show options if you run it without arguments, but I see this is broken - will be fixed next build.) Among other things, it will produce a list of anomalous peaks above 3sigma (set anom_map_cutoff=X to change this), which will also written to a PDB file as UNK atoms (chain C). -Nat
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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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
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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
On Tue, Mar 27, 2012 at 9:22 AM, John Rose
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.
Sorry, my description of the program wasn't entirely accurate. The default settings (inherited from the existing peak search in phenix.refine) are tuned to find *unmodeled* peaks and holes, without significant overlap with existing atoms. (Water molecules are handled separately.) Setting the "Min model peak dist" to 0 will probably allow it to find peaks on top of atoms. This may be somewhat misleading - it would not be difficult to change the default settings for the program if this would make it more useful. -Nat
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John Rose -
Nathaniel Echols