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 PHASER, 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. Note that solutions from Phaser can be used, since they use the same Eulerian angle convention, but the exact syntax will need to be edited to conform to one of the above expected forms.

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 columns labelled #Peak reference the peak numbers in the first table. 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