RFCORR (CCP4: Supported Program)
NAME
rfcorr - Analysis of correlations between cross- and self-Rotation functions.SYNOPSIS
rfcorr MAPIN foo.map PEAKS foo.dat[Keyworded input]
AUTHOR
Ian Tickle, Birkbeck College, London. (tickle@cryst.bbk.ac.uk).DESCRIPTION
To analyse self- and cross-rotation function results for correlations between peak positions. This should help to identify firstly the rotational component(s) of the non-crystallographic symmetry, and secondly the correct peaks in the cross-rotation function. This requires a self-rotation function map calculated either by ALMN or by AMORE, i.e. the angular variables must be Eulerian, not polar (a map produced by POLARRFN will not work), and also a list of peaks from a cross-rotation function map produced by a peak search.INPUT FILES
- MAPIN
-
Eulerian angle self-rotation function map (at least 1 asymmetric
unit) computed by ALMN or AMORE/ROTFUN (SELF option).
- PEAKS
- Peak list of cross-rotation function map produced by ALMN or
AMORE/ROTFUN (CROSS option). Note that if more than 50 peaks are
given, only the first 50 are used. See ALMN keyword.
Example of ALMN format:
PEAK 61.50 20.45 113.50 0.00000 0.00000 0.00000 9.9 0.0
Example of AMORE format:
SOLUTIONRC 1 61.50 20.45 113.50 0.00000 0.00000 0.00000 9.9
Both of these are read in free format, i.e. at least 1 space separating all character and numeric items.
KEYWORDED INPUT
All keywords except SPACEGROUP are optional; default values are assumed for the others. Keywords may appear in any order, except for END which if present must be last. Only the first 4 characters of keywords are significant and all input is case-insensitive.Possible keywords are -
ALMN, ANGLES, CHI, END, NUMPEAK, ORTHOG, PEAK, SPACEGROUP, TITLE
TITLE <Title>
Title for job (max 80 characters).ALMN
Peak list assumed in ALMN format; default is AMORE format.SPACEGROUP <NSG>
Space group name or number; no default. Only the rotational symmetry part of the space group operator is used, so lattice centring and translational components of screw axes are ignored. So, for example, P222, I222, P21212, C2221 etc. will all produce identical results.ORTHOG <NC>
Orthogonalisation code used for the crystal data in ALMN or AMORE; default is 1.PEAK <PL>
Peak limit; map values less then PL times the maximum value in the self-RF are not printed; default is 0.1 .NUMPEAK <NP>
Maximum number of self-RF map values to print; default is 50.CHI <CHI> <TOL>
Chi value to print and tolerance in degrees. This is useful for example to select only map values for 2-fold axes (chi = 180). Note that chi may be called kappa in other programs. If CHI = 0 all chi values > TOL are printed. The defaults are CHI = 0, TOL = 10.ANGLES <NA>
Maximum number of self-RF map points for which inter-rotation axis angles are to be printed; default and maximum is 50.END
Terminate input.PRINTER OUTPUT
The output echoes the input. Then a table of pairs of cross-RF peak index and symmetry index, followed by calculated polar angles theta, phi, chi and self-RF map value are printed sorted in descending order of the latter in one asymmetric unit. Note that theta may be called omega or psi in other programs. Finally the angles between pairs of rotation axis vectors, including symmetry-generated, are printed in 4 columns.EXAMPLES
set verbose
ecalc HKLIN mrenin HKLOUT mrenin_ecalc <<EOD
TITLE ** Ecalc for mouse renin crystal. **
LABI FP=FPmrenin SIGFP=SPmrenin
EOD
amore HKLIN mrenin_ecalc HKLPCK0 mrenin_ecalc.hkl <<EOD
TITLE ** Packing h k l E for mouse renin crystal. **
SORT
LABIN FP=E
EOD
rm mrenin_ecalc.mtz
pdbset XYZIN hexpep XYZOUT hexpep_rfcell <<EOD
SPACEG P1
CELL 80 84 97
EOD
sfall XYZIN hexpep_rfcell HKLOUT hexpep_rfcell <<EOD
TITLE ** Structure factors for hexagonal pepsin in RF cell. **
MODE SFCALC XYZIN
SFSG 1
SYMM 1
RESO 20 3
EOD
ecalc HKLIN hexpep_rfcell HKLOUT hexpep_ecalc <<EOD
TITLE ** Ecalc for hexagonal pepsin model. **
LABI FP=FC
EOD
amore HKLIN hexpep_ecalc HKLPCK0 hexpep_ecalc.hkl <<EOD
TITLE ** Packing h k l E for hexagonal pepsin model. **
SORT
LABIN FP=E
EOD
rm hexpep_rfcell.mtz hexpep_ecalc.mtz
amore HKLPCK0 mrenin_ecalc.hkl HKLPCK1 hexpep_ecalc.hkl \
CLMN0 mrenin.clmn CLMN1 hexpep.clmn MAPOUT mrenin_cross \
>! mrenin_cross.log <<EOD
ROTFUN
TITLE ** Cross rotation function with E's. **
CLMN CRYST ORTH 3 RESO 20 3 SPHERE 35
CLMN MODEL 1 RESO 20 3 SPHERE 35
ROTATE CROSS MODEL 1 NPIC 20
EOD
rm mrenin_cross.map
amore HKLPCK0 mrenin_ecalc.hkl CLMN0 mrenin.clmn \
MAPOUT mrenin_self <<EOD
ROTFUN
TITLE ** Self rotation function with E's. **
ROTATE SELF NPIC 20
EOD
grep SOLUTIONRC mrenin_cross.log >! mrenin_cross.dat
rfcorr MAPIN mrenin_self PEAKS mrenin_cross.dat <<EOD
TITLE ** Mouse renin self/cross rotation function correlation. **
SPACEG p2
ORTH 3
CHI 180
EOD
The output below shows the 222 non-crystallographic symmetry. The first table
echos the 8 input peaks from the cross-rotation function. The second table
shows the positions of the 10 points in the self-rotation function above the
default threshold corresponding to the non-crystallographic 2-fold axes (chi ~=
180) that relate pairs of the highest 4 peaks, including symmetry related,
in the cross-RF. The last table shows the ~90 deg angles between these points
in the self-RF.
Peak Alpha Beta Gamma
1 61.50 20.02 113.50
2 68.33 26.06 107.24
3 112.50 154.69 289.00
4 116.00 157.55 293.50
5 103.14 88.09 166.45
6 70.12 116.85 97.56
7 67.00 105.43 97.30
8 114.90 8.17 100.72
Serial #Peak #Peak(#Symm) Theta Phi Chi self-RF
1 3 4 ( 2) 2 81 179 78.75
2 1 2 ( 2) 3 87 179 51.59
3 2 3 ( 2) 90 180 179 39.46
4 2 3 ( 1) 90 90 180 39.46
5 1 3 ( 2) 90 179 174 37.41
6 1 3 ( 1) 87 89 179 37.41
7 1 4 ( 1) 89 89 179 32.41
8 1 4 ( 2) 89 179 178 32.41
9 2 4 ( 2) 90 179 176 25.68
10 2 4 ( 1) 88 89 179 25.68
Inter-vector angles: Serial[i] Serial[j] (Symm[j]) Angle, in 4 columns.
1 2( 1) 2 1 2( 2) 5 1 3( 1) 90 1 3( 2) 90
1 4( 1) 88 1 4( 2) 89 1 5( 1) 90 1 5( 2) 89
1 6( 1) 89 1 6( 2) 86 1 7( 1) 89 1 7( 2) 87
1 8( 1) 90 1 8( 2) 89 1 9( 1) 90 1 9( 2) 89
1 10( 1) 86 1 10( 2) 90 2 3( 1) 90 2 3( 2) 90
2 4( 1) 86 2 4( 2) 87 2 5( 1) 90 2 5( 2) 90
2 6( 1) 90 2 6( 2) 84 2 7( 1) 88 2 7( 2) 86
2 8( 1) 90 2 8( 2) 89 2 9( 1) 90 2 9( 2) 89
2 10( 1) 85 2 10( 2) 89 3 4( 1) 90 3 4( 2) 90
3 5( 1) 1 3 5( 2) 1 3 6( 1) 89 3 6( 2) 89
3 7( 1) 89 3 7( 2) 89 3 8( 1) 1 3 8( 2) 1
3 9( 1) 0 3 9( 2) 1 3 10( 1) 90 3 10( 2) 90
4 5( 1) 89 4 5( 2) 89 4 6( 1) 3 4 6( 2) 2
4 7( 1) 2 4 7( 2) 1 4 8( 1) 89 4 8( 2) 89
4 9( 1) 90 4 9( 2) 90 4 10( 1) 2 4 10( 2) 3
5 6( 1) 90 5 6( 2) 90 5 7( 1) 90 5 7( 2) 90
5 8( 1) 0 5 8( 2) 1 5 9( 1) 0 5 9( 2) 1
5 10( 1) 90 5 10( 2) 90 6 7( 1) 2 6 7( 2) 4
6 8( 1) 90 6 8( 2) 90 6 9( 1) 90 6 9( 2) 90
6 10( 1) 5 6 10( 2) 1 7 8( 1) 90 7 8( 2) 90
7 9( 1) 89 7 9( 2) 89 7 10( 1) 3 7 10( 2) 1
8 9( 1) 1 8 9( 2) 1 8 10( 1) 89 8 10( 2) 89
9 10( 1) 90 9 10( 2) 90