#!/bin/sh # First calculate structure factors for model coordinates in P1 cell. # Dont forget to change the CRYSTL and SCALEi cards at the head # of the PDB file to those appropriate for the "P1 " model cell. # eg: for a cell 50*50*50 you need this. #CRYST1 50.00 50.00 50.00 90.00 90.00 90.00 #SCALE1 0.020000 0.000000 0.000000 0.00000 #SCALE2 0.000000 0.020000 0.000000 0.00000 #SCALE3 0.000000 0.000000 0.020000 0.00000 # toxd_mod_p1.pdb obtained from toxd.pdb by # 1) changing CRYSTL and SCALEi cards # 2) removing water molecules. # this has been done with the supplied version set -e # Read in coordinates to calculate structure factors. sfall HKLOUT $CCP4_SCR/toxd_mod_p1 \ XYZIN $CEXAM/unix/runnable/toxd_mod_p1.pdb <<-END-sfall TITL Phasing on toxd from test data area MODE SFCALC XYZIN RESO 100 3 SFSG 1 SYMM 1 LABO FC=FC_p1 PHIC=PHIC_p1 NAME PROJECT TOXD CRYSTAL MODEL DATASET CALCULATED END END-sfall # # Generate E values for Observed F's ( Ian Tickle says so) # ecalc hklin $CEXAM/toxd/toxd hklout $CCP4_SCR/toxd_e.mtz <<-EOF TITLE TEST OF PROGRAM ECALC WITH REFLECTION DATA REFLECTIONS 1500 RESOLUTION 0 LABIN FP=FTOXD3 SIGFP=SIGFTOXD3 EOF # # Generate E values for Calculated F's # ecalc hklin $CCP4_SCR/toxd_mod_p1 hklout $CCP4_SCR/toxd_mod_p1_e <<-EOF TITLE TEST OF PROGRAM ECALC WITH REFLECTION DATA REFLECTIONS 1500 RESOLUTION 0 LABIN FP=FC_p1 EOF # # Then run ALMN # almn HKLIN $CCP4_SCR/toxd_e HKLIN2 $CCP4_SCR/toxd_mod_p1_e \ MAPOUT $CCP4_SCR/almn.map <<-END-almn CROSS 3 15 RESO 10 3.4 TITL Toxd model rotation function. CRYS file 1 orth 1 flim 1 10000000000000 LABI FILE 1 F=E CRYS file 2 orth 1 flim 1 10000000000000 LABI FILE 2 F=E LIMIT 0 90 5 1 ! Beta limit 90 because of symmetry ! If in doubt set Beta limit 180.. FIND 5 20 NOPR MAP END END-almn #