The Native Patterson Map
Performing the Calculation with XtalView

A section of the native Patterson map, Z=0.
Calculated with XtalView. Map courtesy of S. Lee.
The native Patterson map is simple to calculate. The only requirements are: the crystal's unit cell parameters, your spacegroup operators, and your data set output by scalepack.

I typically use the program xfft from 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 the setup . XtalView is an especially useful suite of programs if you are solving a structure de novo. I find it indispensible for looking at isomorphous difference Patterson maps and anomalous difference Patterson maps. So, I think it is worth the time. If you are setup to use CCP4 programs, you can calculate a native Patterson with CCP4's fft program instead.

Manual for XtalView: Manpages or User guide

Reference for XtalView:
D. E. McRee, Practical Protein Crystallography, 2nd edition,ISBN: 0-12-486052-4, 1999.

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

INSTRUCTIONS FOR CALCULATING NATIVE PATTERSON WITH XtalView
EXAMPLES
If you are setup to use XtalView, you may proceed as follows. If not, go here .
STEP ONE

Use xprepfin to convert your scalepack file to .phs format. In this example type:

xprepfin dhfr.sca dhfr.phs

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

Then press the "Apply" button.
You should now have a .phs file in your directory.

STEP TWO

Use xfft to convert your .phs file to a Patterson map. In this example type:

xfft dhfr.phs dhfr.map

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.


STEP THREE

Display map with xcontur. In this example type:

xcontur dhfr.map

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 read the peak height by simply clicking on the peak.

Be sure to select x, y, and z limits that cover your asymmetric unit.

Xprepfin window, used in step one.




Xfft window, used in step two.







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