The Isomorphous Difference Patterson Map
Performing the Calculation with XtalView
Harker sections from an isomorphous difference Patterson map. 
T7 helicase domain ethylmercurythiosalicylate derivative. Spg P61
The Isomorphous 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 isomorphous difference Patterson map. 

The crystal's unit cell parameters, spacegroup operators, native and derivative data sets output by scalepack.

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 Isomorphous 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 scalepack file for the native crystal ( to .fin format (native.fin). In a unix window, type: 

xprepfin native.fin

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

Then press the "Apply" button.
You should now have a .fin file in your directory. Repeat this step with the derivative scalepack file to create a fin file. For example: 

xprepfin hg.fin


Use xmerge to merge your native.fin and hg.fin files into a double fin file (e.g. isomorphous.df). In a unix window, type:

xmerge native.fin hg.fin isomorphous.df

Since we have plenty of reflections we can set the slider to 20 bins:

Press "Single" meaning that a single scale factor will be used. You may also want to try "anisotropic" to get a better fit, but beware, sometimes this fails. Check the R-factors with xstat. In a unix window type:

xstat isomorphous.df 

Select: R-factor vs. resolution
Select: |F1-F2| vs. resolution

Then press the Graph It button.

You will get two windows:
1) plot of the isomorphous Rfactor
2) plot of the isomorphous difference.

These windows will indicate if the scaling is correct and suggest a resolution range to use in the isomorphous difference Patterson map.


In a unix window, type:

xfft isomorphous.df

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

Type in your resolution range. 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 7 sigma (level 350).

Xprepfin window, used in step one.

Xmerge window, used in step two.


Xfft window, used in step three.


Xcontur window, used in step four.



[Overview] · [Facilities] · [People] · [Services] · [Lectures] · [BioLinks] · [Stats] · [Search]