![]()
|
RFCORR (CCP4: Supported Program)NAMErfcorr - Analysis of correlations between cross- and self-Rotation functions.SYNOPSISrfcorr MAPIN foo.map PEAKS foo.dat[Keyworded input] AUTHORIan Tickle, Birkbeck College, London. (tickle@cryst.bbk.ac.uk).DESCRIPTIONTo 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
KEYWORDED INPUTAll 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).ALMNPeak 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.ENDTerminate input.PRINTER OUTPUTThe 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.EXAMPLESset 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 EODThe 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 SEE ALSOCalculation of rotation function: |