GETAX (CCP4: Supported Program)
GETAX - real space correlation search
Real space searching for rotation axis of a D<n> or C<n> multimer (
<n> = 2,3,4,5,6,... ).
If you have:
you can start using this program to find the translational part of
your NCS operators.
It has worked in several cases with even very poor phases ( 20
molecules/au, <fom>=0.25 to about 6Å resolution).
Version 2.5 (14. April 1998)
getax MAPIN foo.map
[ XYZIN foo1.pdb ] [ XYZOUT foo2.pdb ]
[ MAPOUT bar.map ]
GETAX is a program to search for your non-crystallographic
symmetry if a first map is available. The only knowledge you
need is a selfrotation solution (from e.g. POLARRFN) and a crude
knowledge of the size/shape of your molecule(s).
map covering a whole unit cell with axis order X=fast,
Y=medium, Z=slow changing index.
This map can be a 6 Angstroem MIR map on a 2 Angstroem grid.
So if you use fft you don't have to worry about getting the
grid right, since fft takes 1/3rd of the high resolution
anyway. Sometimes it can be helpful to try finer grid spacings
(this slows down the calculation, though).
Depending on your spacegroup, you will have to change the
extent and/or axis order with MAPMASK.
a PDB file with an initial model for the correlation search.
see: INPUT XYZ
a PDB file with the initial search sphere/slice as build and
used by GETAX.
This can be a PDB file with orthogonal coordinates either before (OUTPUT XYZ) or after initial
interpolation (OUTPUT GXYZ).
To be sure that everything works fine: have a look at this
output file with your favourite graphics program (O or RASMOL or
whatever ...): there should be no overlap between the segments
and the rotation axis should be properly oriented.
is an output map with correlation coefficients at each grid
point. There are two possible correlation coefficients:
This is the most important output: you can read it into PEAKMAX to
extract peak positions which correspond to centers of your
rotation axis. Or even better: use your favourite
graphics program (e.g. O) and look for high peaks and/or long
stretches of "density".
Available keywords are:
POLAR <omega> <phi> <kappa> [<omega-2> <phi-2> [<kappa-2>] ]
Polar angles of a selfrotation solution (definition as in
Combining two selfrotation solutions:
If you have a twofold perpendicular to your rotation axis
(e.g. D4 symmetry) you can give the polar angles as <omega-2>
and <phi-2> (<kappa-2> defaults to 180.0). A corresponding
sphere/disk will be built. The program stops if the two
rotations aren't perpendicular. If they are perpendicular within
an error of 5 degrees, the program calclulates a new 2-fold which
now is exactly perpendicular, thus correcting possible rounding
errors of e.g. POLARRFN.
Polar angles given on POLAR card are for orthogonalization code
ncode = orthogonalization code:
SPHERE <outer-radius> [<inner-radius>]
defines a spherical shape of your multimer.
Builds a sphere with radius <outer-radius>. You can omit a
smaller inner sphere by giving <inner-radius>.
The sphere will be divided into <ifold> segments (where
<ifold> is determined by <kappa>) and rotated so that its
rotation axis is parallel with the selfrotation axis and its center
is at (0 0 0). You can write this sphere out to logical XYZOUT.
To get a rough idea what your protein looks like: use the molecular
weight Mr to get radius of assumed spherical protein:
1.23 * Mr * 0.75
radius = ( ---------------- ) ^ 0.333
default: <outer-radius>=25. <inner-radius>=0.
SLICE <outer-radius> <height> [<inner-radius>]
defines a different shape of your multimer.
Builds a disk with outer radius <outer-radius> and height
<height>. You can omit a smaller inner circle by giving
The disk will be divided into <ifold> segments (where
<ifold> is determined by <kappa>) and rotated so that its
rotation axis is parallel with the selfrotation axis and its
center is at (0 0 0). You can write this disk out to logical
default: <outer-radius>=25. <height>=15. <inner-radius>=0.
CHECK [[NO]CORR] [[NO]PACK] [[N]AX1/[N]AX2/[N]AX3/[N]AX4]
which checks to perform:
AX2 and AX3 don't make any difference in the result
(but AX3 keeps the absolute values of the output
correlation map at a reasonable height).
defaults: CORR NOPACK AX4
SKIP [AUTO <askip>]/[<iskip>]
Saves CPU time by using only a limit number of the points
describing a sphere/slice.
Takes only every <iskip>th point of each segment in your
sphere/disk to compute correlation coefficients. This is a
good idea if your sphere/disk is rather big. It can save a lot
of CPU. But take care that you keep at least ~500 points in
If keyword AUTO is present, the actual value of iskip is set
so that approximately <askip> points per segment are used.
default: AUTO 500
Step along each cell axis (in grid units).
Unless you have calculated your map on a very fine grid,
it does make things worse. And perhaps you'll miss the right
solution !! It doesn't save a lot of CPU, since we have to
interpolate the values at the end anyway.
Correlation coefficients will only be calculated if the density
for all segments in the sphere/disk is .gt. <minden>*sigma.
The default is also a very reasonable value.
XYZLIMIT <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>
Limits (in grid points) for search.
Unless you know already where to look for your multimer, I would always search
the whole unit cell.
default: whole unit cell
OUTPUT [XYZ/GXYZ] [MAP/NOMAP] [SMAP]
read in PDB file to define the shape of your molecules.
If you have a pretty good idea what your molecule looks like
and how it is oriented (but not positioned) this could be quite
helpful. But some restrictions:
REPORT <report> <top>
Not only reports the maximum correlation found so far, but also
every correlation .gt. <report>.
At the end of the search the found correlations are sorted
according to height and the <top> number is reported.
default: <report>=1. <top>=20
A unix example script for performing a simple NCS search can be
found in $CEXAM/unix/non-runnable/
though it will need to be edited before use.
- C. Vonrhein and G. E. Schulz, Acta Cryst., D55, 225 - 229 (1999)
Locating proper non-crystallographic symmetry in low-resolution
electron-density maps with the program GETAX.
peakmax(1), dm(1), ncsmask(1).
Last modification: 24.10.2013