RSEARCH (CCP4: Supported Program)
NAMErsearch - R-factor and correlation coefficient between Fcalc and Fobs for positions of molecule within a specified grid.
SYNOPSISrsearch HKLIN foo_in.mtz [ SEARCHSAVE foo_search.tmp ] [ MAPOUT foo_rsearch.map ]
DESCRIPTIONWhen a molecule is correctly orientated in a unit cell, but the translation parameters are not known, RSEARCH calculates the R-factor and correlation coefficient between calculated and observed structure factors for each position of the molecule within a specified grid.
You may prefer to calculate a translation function with TFFC instead of RSEARCH, since this is much faster.
There is an option to restart RSEARCH when it runs out of time : a file assigned to SEARCHSAVE will record the intermediate sums for the R factors. These are updated after every 100th reflection and a note is written to the log file. There are also options (keywords CENT and RZONE) to limit the reflections used to centrics or a specified zone.
KEYWORDED INPUTThe various data control lines are identified by keywords. Only the first 4 characters need be given. Those available are :
AXIS, BINMAP, BGRV, CENT, CORRELATION, END, FCLIMIT, FOLIMITS, LABIN, LPMAP, NRFACTOR, RESOLUTION, RESTART, RZONE, SCALE, SYMMETRY, TITLE, XGRID, YGRID, ZGRID
AXISOrder of grid axes : fast, medium, slow.
At present, the program only looks at the slow (sectioning) axis. Possible inputs are therefore
- X Y Z - Z X Y - Y Z X
BINMAPOutput a map of R factors or correlation coefficients over the specified grid
BGRV <brgval>Background R value for maps.
Default: the average R value.
The terms calculated are (background R value - grid R value).
CENTBy default, all reflections are included in the calculation. If this is set, ONLY centric reflections are selected. Centric zones are identified using the spacegroup operators.
CORRELATIONTurns ON the plotting of correlation maps
FCLIMIT <fmaxc>Set lower limit on FC for inclusion in R factor calculation.
In low symmetry space groups such as P21, you should exclude all terms where one calculated (partial) structure factor FC is very small, since then the R factor will be independent of translation.
FOLIMITS <fmin> <fmax>Set upper and lower limits on observed structure factors for inclusion in R factor calculation (given in either order).
LABIN <program label>=<file label>...Input column assignments. The program labels are:
H K L FP SIGFP FC1 PC1 ... FC12 PC12 FC PHICFP is the observed structure factor and SIGFP its standard error. FCn and PCn are the partial calculated structure factors and phases for symmetry operation n. Known structure may be added in by defining FC and PHIC.
LPMAPOutput a lineprinter map of R factors for all hkl and for each of 5 resolution shells.
NRFACTOR <nrfactor>Number of R factors to be listed to output file. Default is 15; maximum is 500.
RESOLUTION [ <resmin> ] <resmax>Low and high resolution limits in either order. These are in Angstroms or 4(sintheta/lambda)**2 if both are <1.0. Defaults: 1000.0 2.0
RESTART <nref> <ihh> <ikk> <ill>Intermediate results will have already been written to a file assigned to SEARCHSAVE. Calculation is restarted after the <nref>-th reflection; <ihh> <ikk> <ill> are the indices of the first reflection to be included. These 4 numbers are printed to the log file after every 100 reflections.
RZONE <number>...5 numbers to define a reflection zone limiting reflections included in the R value calculation.
To define the zone -h +k +l = 3n input RZON -1 1 1 3 0 To define l = 2n +1 input RZON 0 0 1 2 1This keyword may be given more than once, but at present ALL conditions must be obeyed simultaneously.
SCALE <scale> <bfact>The scale and temperature factor to be applied to observed structure factors FP. Defaults: 1.0 0.0.
FP(USED) is scale*FP(INPUT)*EXP(-bfact(SINTHETA/LAMBDA)**2).
It is sensible to run SCALEIT to put FP onto the same scale as one of the (partial) structure factors FCn before running RSEARCH. The scale here should then be approximately sqrt(nsymp), where nsymp is the number of primitive symmetry operators.
SYMMETRY [ <nspgrp> | <namspg> ]Spacegroup number or name. You may alternatively input operators in X,Y,Z form. Spacegroup details are normally taken from the input MTZ file.
TITLE <title>A title to be written to the log file.
XGRID | YGRID | ZGRID <min> <max> <n>3 parameters for each of the 3 keywords: XGRID, YGRID and ZGRID.
The input is complicated to allow greater flexibility in describing the search volume. The first 2 parameters give the range in grid points, either directly or by reference to other limits given; the third, the number of grid points covering the unit cell in the appropriate direction.
For a simple rectangular box : XGRID ixmin ixmax nx (3 numbers) YGRID iymin iymax ny (3 numbers) ZGRID izmin izmax nz (3 numbers) For a prism, there are many options. For example : XGRID ixmin ixmax nx (3 numbers) YGRID xmin iymax ny (1 character string, 2 numbers) (or YGRID iymin xmax ny ) (number, character string, number) (or YGRID xmin xmax ny ) (2 character strings, 1 number) ZGRID izmin izmax nz (3 numbers) where xmin means type the letters xmin .... For another sort of prism : XGRID ixmin ixmax nx (3 numbers) YGRID xmin iymax ny (1 character string, 2 numbers) (or YGRID iymin xmax ny ) (number, character string, number) (or YGRID x x ny ) (2 character strings, 1 number) ZGRID izmin izmax nz (3 numbers) (or ZGRID xmin izmax nz ) (character string, 2 numbers) (or ZGRID izmin xmax nz ) (number, character string, number) (or ZGRID x x nz ) (2 character strings, 1 number) (or ZGRID ymin izmax nz ) (1 character string, 2 numbers) (or ZGRID izmin ymax nz ) (number, character string, number) (or ZGRID y y nz ) (2 character strings, 1 number)Note that maps can only be output if the grid is rectangular. The maximum total grid points in the search volume is 60000. The maximum number in any one direction is 1024.
ENDEnd of input.
INPUT AND OUTPUT FILES
INPUT : MTZ Data file assigned to HKLIN [File containing intermediate sums assigned to SEARCHSAVE] OUTPUT :[File for Binary R factor map assigned to MAPOUT] Those in parentheses are optional.
Memory allocationThe program allocates memory dynamically. If the default isn't enough you can increase it by setting the logical name RSEARCH_NSIZE to the appropriate value indicated by the error message. (It ought to figure this out for itself.)
Suggested procedure leading to RSEARCH
EXAMPLESFor previous stages to this, see 'NOTES'
# Rfactor search # Input mtz hkl list of FP SIGFP FC1 PC1 FC2 PC2..... # R factor requires FP scaled to FC. # Correlation coefficient should be independent of scale. # rsearch HKLIN cad_sc.mtz MAPOUT dav.map SEARCHSAVE dav.tmp << END-r TITLE Bacillus search in a-c plane SCALE FP 1.414 0 RESOLUTION 8 4 ! resolution limits FOLIMITS 10 10000000000. ! Fobs limits FCLIMIT 50 ! Fc minimum CORRELATION BINMAP ! binary map output AXIS Y Z X XGRID 0 20 40 ! grid limits YGRID 0 1 1 ZGRID 0 40 80 LABIN FP=F SIGFP=SIGF FC1=FC1 PC1=AC1 FC2=FC2 PC2=AC2 END END-r
AUTHOREleanor Dodson, York University