The Anomalous Difference Patterson Map
Performing the Calculation with XtalView

Harker sections from an anomalous difference Patterson map. T7 helicase domain ethylmercurythiosalicylate derivative. Note: Harker sections of the anomalous difference Patterson map are noisier than in the isomorphous difference Patterson map because this particular data set was not collected at the peak wavelength for mercury. Sadly, the data was collected at a non-tunable beam line (CHESS A1) Space group P61.
The Anomalous Difference Patterson map is simple to calculate with the XtalView suite of programs. The program produces a contoured map, which may be displayed and re-contoured interactively in sections along x, y, or z. There is a small investment in time to setup to use XtalView (10 minutes). However, you only have to do it once. I have constructed a web page to assist you in setting up to use XtalView. Once you have setup, then follow the steps outlined below for producing an anomalous difference Patterson map. 

The crystal's unit cell parameters, spacegroup operators, and derivative data set output by scalepack with the "anomalous" flag or "scale anomalous" flag .

Manual for XtalView:Manpages or User guide

Reference for XtalView:
D. E. McRee, Practical Protein Crystallography, 2nd edition,ISBN: 0-12-486052-4, 1999. Only $79.95 what a bargain!

Reference for the Anomalous difference Patterson Map:
J. Drenth, Principles of Protein X-Ray Crystallography (Springer Advanced Texts in Chemistry) Hardcover (February 1999). See pages 130-139.

If you are setup to use XtalView, you may proceed as follows. If not, go here .


Use xprepfin to convert your ANOMALOUS scalepack file for the derivative crystal ( to .fin format (hg_anom.fin). In a unix window, type: 

xprepfin hg_anom.fin

Choose the buttons such that:
Input Format: .sca
Convert I to F: Yes
Data are: Bijvoet pairs
Output Format: .fin 

Then press the "Apply" button.
You should now have a .fin file in your directory. It should have anomalous pairs in columns side by side.


Convert your anomalous fin file (hg_anom.fin) into a double fin file (e.g. anomalous.df). In a unix window, type:


At the prompt, type the name of the input fin file:


then type the name of the output df file:



In a unix window, type:

xfft anomalous.df

Choose the buttons such that:
Map Type:Fo*Fo (Patterson)

Type in your resolution range. Outlier filter should be set to a value between 33% and 50% when using anomalous differences. Be sure to press Enter everytime you enter a new number.

Press Read Phase File
then press Calculate

Xfft will automatically select grid units appropriate for your unit cell and resolution.
You should now have a .map file in your directory.


Display map with xcontur. In a unix window type:


Press the "next" button to page through the sections of your map. Look for peaks over 5 sigma. The maps are automatically scaled so that a peak height of 50 is equal to 1 sigma. So look for peaks of height 250 (5 sigma). You can determine the peak height by simply clicking on the peak.

Be sure to select x, y, and z limits that cover your asymmetric unit. If you want to see the whole unit cell, chose limits of 1.0 for rows and columns. In this example, the space group is P61, so there are three harker sections, (z=.166, z=.333, z=.500). The example window on the right, is set to view the Harker section at z=.333, a cross section through the unit cell. The map section should look like one of the sections in the image displayed at the top of this file. The contour levels start at 1 sigma and the intervals are set at one sigma. The highest peak on the Harker section is about 4 sigma (level 200). Unfortunately, this data set was collected at CHESS beamline A1, where the wavelength was not tunable. Therefore, the anomalous signal is rather weak compared to what it could have been, if tuned to the Hg peak wavelength.

Xprepfin window, used in step one.

Xfft window, used in step three.


Xcontur window, used in step four.



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