#!/bin/sh # 1) Read in coordinates to calculate structure factors. # Use sf_calc to produce $CCP4_SCR/toxd_sf1.mtz # 2) Read in coordinates to calculate solvent density map. # Read in map to calculate "solvent" structure factors # in $CCP4_SCR/toxd_sf_solv # 3) Use icoefl to scale SFs and solvent transform together. # No guarantee this will work sensibly; I dont know what to expect.. # (in fact, the converged parameters don't look v. sensible, # but you get the idea). set -e # Read in coordinates to calculate structure factors. sfall \ HKLIN $CEXAM/toxd/toxd \ HKLOUT $CCP4_SCR/toxd_sf1 \ XYZIN $CEXAM/toxd/toxd.pdb \ << END-sfall TITLE Structure factors calculated for toxd. GRID 152 96 64 !div CELL by these should give .=. 0.7 A MODE SFCALC XYZIN HKLIN RESOLUTION 37 2.1 BINS 60 RSCB 8.0 2.1 LABIN FP=FTOXD3 SIGFP=SIGFTOXD3 - F0=FAU20 F1=SIGFAU20 - F2=FMM11 F3=SIGFMM11 - F4=FI100 F5=SIGFI100 LABOUT FC=FC_sf PHIC=AC_sf END END-sfall # Calculate solvent map from atom coordinates # and then generate structure factors from map # sfall \ XYZIN $CEXAM/toxd/toxd.pdb \ MAPOUT $CCP4_SCR/toxd_solv \ << END-sfall TITLE Calculating "coordinate" map GRID 152 96 64 !div CELL by these should give .=. 0.7 A MODE ATMMAP SOLVMAP RESOLUTION 37 2.1 BINS 60 RSCB 8.0 2.1 SYMMETRY 19 END END-sfall # Read in map to calculate "solvent" structure factors. sfall \ HKLIN $CCP4_SCR/toxd_sf1 \ HKLOUT $CCP4_SCR/toxd_sf_solv \ MAPIN $CCP4_SCR/toxd_solv \ << END-sfall TITLE calculating structure factors from "Fc" map GRID 152 96 64 !div CELL by these should give .=. 0.7 A MODE SFCALC MAPIN HKLIN RESOLUTION 37 2.1 BINS 60 RSCB 8.0 2.1 LABIN FP=FTOXD3 SIGFP=SIGFTOXD3 LABOUT ALLIN FC=FC_solv PHIC=AC_solv END END-sfall # Scale icoefl \ HKLIN $CCP4_SCR/toxd_sf_solv.mtz \ hklout $CCP4_SCR/toxd_sf2.mtz \ << eof title Scale Fc(atom) and Fc(solvent) to Fobs labin FP=FTOXD3 SIGFP=SIGFTOXD3 FC1=FC_sf PHIC1=AC_sf - FC2=FC_solv PHIC2=AC_solv labout FC=FCALL PHIC=PHICALL scale FP 1.4 scale FC1 1.0 15.0 scale FC2 1.0 0.0 # default cycles 20 eof #