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.
AXIS, BINMAP, BGRV, CENT, CORRELATION, END, FCLIMIT, FOLIMITS, LABIN, LPMAP, NRFACTOR, RESOLUTION, RESTART, RZONE, SCALE, SYMMETRY, TITLE, XGRID, YGRID, ZGRID
- X Y Z - Z X Y - Y Z X
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.
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.
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.
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.
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.
# # ***************************************************************** # # Run sfall to calculate structure factors # sfall HKLOUT sfrkall.mtz XYZIN trans_pgk.pdb << END-sfall TITLE SFS MODE SFCALC XYZIN GRID 80 160 160 RESOLUTION 20 3 SYMMETRY 1 SFSGRP 1 LABOUT FC=FC PHIC=AC END END-sfall # # ***************************************************************** # # Run cad to collect FP and FC's into one file. # Up to this stage, can use the same procedure for TFFC & RSEARCH. # No phase changes made to partial phases. # cad HKLIN1 allderiv.mtz HKLIN2 sfrkall.mtz HKLOUT cad.mtz << END-cad RESOLUTION OVERALL 20 3 TITLE resolving the bacillus pgk LABIN FILE 1 E1=F E2=SIGF CTYPIN FILE 1 E1=F E2=Q LABIN FILE 2 E1=FC E2=AC CTYPIN FILE 2 E1=U E2=V END END-cad # # ***************************************************************** # # Optional step # Run scaleit to put FP onto the same scale as one of the FC's. # Remember you will need to use the resolution required for RSEARCH. # scaleit HKLIN cad.mtz HKLOUT cad_sc.mtz << END-scaleit TITLE Scale FP to one FCpart ready for RSEARCH RESOLUTION 8 4 REFINE isotropic LABIN FP=FC1 SIGFP=FC1 FPH1=F SIGFPH1=SIGF CONVERGE ABS 0.0001 TOLR 0.000000001 NCYC 4 END END-scaleit
# 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