The Self Rotation Function
Performing the Calculation with GLRF
A section of the self rotation function, Kappa=180. 
Calculated with GLRF. Map courtesy of S. Lee. 
 The self rotation function is easy to perform. 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 GLRF from the Replace suite of programs written by Liang Tong. The program produces a contoured map in postscript format that is easily interpreted. An example of a typical input file is given below. Cut and paste the script into a file called self.com. Edit it for your crystal. Execute the file by typing "self.com". View the file "self.ps" with xpsview, showps, display, gs, or whatever postscript interpreter you like. View the sections of Kappa. 

Manual for GLRF:
/joule2/programs/glrf/Glrf/glrf.ps.

Reference for GLRF:
L. Tong & M. G. Rossmann, Methods in Enzymology 276, 594-611, 1997.

GLRF  home page

Reference for the Self Rotation Function:
M. G. Rossmann and D. M. Blow, Acta Cryst. 15, 24-31, 1962.
INSTRUCTIONS FOR CALCULATING The Self Rotation Function with GLRF
COMMENTS

#!/bin/csh -f
/joule2/programs/bin/glrf <<EOF
!
Title the Self Rotation Function calculation
print self.prt
!
!Conventions
!
polar xyk
euler zyz
orthogonalization axabz
!
!
! Crystal A
!
acell 52.4 52.4 105.3 90.0 90.0 120.0
asymmetry x, y, z
asymmetry -y, x-y, z
asymmetry -x+y,-x,z
asymmetry -y,-x,-z
asymmetry -x+y,y,-z
asymmetry x,x-y,-z

aobs-file scalepack.sca
aformat (3i4, 2f8.2)
acutoff 2 1 0
apower 1
nshell 8
origin  false !Patterson origin removal!
cutoff 2.0                 !Large term cutoff
!
! Search parameters
!
self true
cross false
fast true
resolution 9.0 6.0
radius 15
rcutoff 25
boxsize 3 3 3
gevaluation 2
sangle polar
slimits 1 0 180 5
slimits 2 0 180 5
slimits 3 0 180 5
peak-cutoff 1 50
oangle polar xyk
section 213
mapfile self.map
!contour your peaks..........................
cntfile self.ps
cntlevel 450.0 1000.0 50
cntsection 1 37
!
stop
EOF

 Important: delete the header from your scalepack file.

self.prt is the log file. It contains a list of the peaks found in the self rotation function.

Use these conventions; they are consistent with those used by CCP4 programs.
 
 
 
 

unit cell parameters for your crystal
 

symmetry operations of your crystal's space group WITHOUT fractional translations! The space group in this example is P3112.
 

aobs-file. Name of the file containing your scalepack data (intensities not structure factors in this example)
 
 
 
 
 
 
 
 

resolution. You should experiment with the resolution range. (e.g. 9-4, 9-5, 8-4, etc.) If your molecules are relatively floppy, peaks in the RF may only be seen at lower resolution.

radius of integration. Again, experiment with this parameter. Use values between the radius and diameter of your protein molecule.

slimits. Let phi, psi, and kappa vary from 0 to 180. Use 5 degree intervals
 
 
 

cntlevel. Contour all peaks above the 450 level, where the highest peak is scaled to the 1000 level. Show intervals of 50.
 
 
 
 

 

 

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