#!/bin/sh set -e # Phasing the rnase using Pt sites only. # See Sevcik, Dodson and Dodson, Acta Cryst. B47 240 (1991) bp3 HKLIN $CEXAM/rnase/rnase25.mtz \ HKLOUT $CCP4_SCR/rnase_phase_mir.mtz << eof-bp3 # native crystal Xtal NATIVE DName NATIVE COLUmn F=FNAT SF=SIGFNAT # platinum derivative Xtal Platinum ATOM Pt XYZ 0.566 0.828 0.018 OCCU 0.2 BISO 25.0 ATOM Pt XYZ 0.842 0.944 0.469 OCCU 0.2 BISO 25.0 ATOM Pt XYZ 0.103 0.941 0.189 OCCU 0.2 BISO 25.0 ATOM Pt XYZ 0.190 0.005 0.742 OCCU 0.2 BISO 25.0 ATOM Pt XYZ 0.047 0.848 0.273 OCCU 0.2 BISO 25.0 DNAME Plat COLUmn F=FPTNCD25 SF=SIGFPTNCD25 # Note! - to add anomalous data, run mtzMADmod to get F+/F- # then, input F+ and F- columns to bp3 ALLIn eof-bp3 # remove this line if you want to run all three exit ############################################################## # example 2 bp3 HKLIN $CEXAM/tutorial/data/gere_MAD_nat_scaleit1.mtz \ HKLOUT $CCP4_SCR/gere_MAD_phase.mtz << eof-bp3 # native Xtal NATIVE DNAMe NATIVE COLU F=F_native SF=SIGF_native # selenium Xtal DER1 ATOM Se XYZ 0.567606 0.19651 0.117643 OCCU 0.1 BISO 25.0 ATOM Se XYZ 0.637982 0.0428475 0.217668 OCCU 0.1 BISO 25.0 ATOM Se XYZ 0.469871 0.255659 0.23827 OCCU 0.1 BISO 25.0 ATOM Se XYZ 0.49385 0.188126 0.41977 OCCU 0.1 BISO 25.0 ATOM Se XYZ 0.794401 0.401274 0.137605 OCCU 0.1 BISO 25.0 ATOM Se XYZ 0.716238 0.238362 0.0869784 OCCU 0.1 BISO 25.0 ATOM Se XYZ 0.259739 0.00855349 0.239787 OCCU 0.1 BISO 25.0 ATOM Se XYZ 0.343637 0.168551 0.319304 OCCU 0.1 BISO 25.0 ATOM Se XYZ 0.173773 -0.0720953 0.391003 OCCU 0.1 BISO 25.0 ATOM Se XYZ 0.179076 0.0804735 0.520765 OCCU 0.1 BISO 25.0 ATOM Se XYZ 0.926494 0.231291 0.18954 OCCU 0.1 DNAME INFL COLUmn F+=F_infl(+) SF+=SIGF_infl(+) F-=F_infl(-) SF-=SIGF_infl(-) FORM Se FP=-6.0 FPP=2.0 DNAME LRM COLUmn F+=F_lrm(+) SF+=SIGF_lrm(+) F-=F_lrm(-) SF-=SIGF_lrm(-) FORM Se FP=-3.0 FPP=3.0 DNAME PEAK COLUmn F+=F_peak(+) SF+=SIGF_peak(+) F-=F_peak(-) SF-=SIGF_peak(-) FORM Se FP=-4.0 FPP=4.0 DNAME HRM COLUmn F+=F_hrm(+) SF+=SIGF_hrm(+) F-=F_hrm(-) SF-=SIGF_hrm(-) FORM Se FP=-3.0 FPP=1.0 ALLIn eof-bp3 ############################################################## # example 3 bp3 HKLIN $CEXAM/toxd/toxd.mtz \ HKLOUT $CCP4_SCR/toxd_phase_mir.mtz \ << eof-bp3 # native crystal Xtal NATIVE Dname NATIVE COLUmn F=FTOXD3 SF=SIGFTOXD3 # silver derivative Xtal SILVER ATOM Au XYZ 0.177 0.104 -0.114 OCCU 0.2 BISO 30.0 ATOM Au XYZ 0.218 0.138 -0.105 OCCU 0.2 BISO 30.0 DNAMe AU COLUmn F=FAU20 SF=SIGFAU20 # Note! - to add anomalous data, run mtzMADmod to get F+/F- # then, input F+ and F- columns to bp3 # mercury derivative XTAL MERCURY ATOM Hg+2 XYZ 0.180 0.294 0.089 OCCU 0.2 BISO 30.0 DNAMe HG COLUmn F=FMM11 SF=SIGFMM11 # iodine derivative Xtal IODINE ATOM I-1 XYZ 0.491 0.370 0.487 OCCU 0.2 BISO 30.0 DNAMe IO COLUmn F=FI100 SF=SIGFI100 ALLIn eof-bp3 ############################################################## # Example 4 # 2 wavelength MAD bp3 HKLIN $CEXAM/tutorial/data/gere_MAD_nat.mtz \ HKLOUT $CCP4_SCR/gere_MAD_phase.mtz << eof-bp3 # MAD data Xtal DER1 ATOM Se XYZ 0.567606 0.19651 0.117643 OCCU 0.5 BISO 50.0 ATOM Se XYZ 0.637982 0.0428475 0.217668 OCCU 0.5 BISO 50.0 ATOM Se XYZ 0.469871 0.255659 0.23827 OCCU 0.5 BISO 50.0 ATOM Se XYZ 0.49385 0.188126 0.41977 OCCU 0.5 BISO 50.0 ATOM Se XYZ 0.794401 0.401274 0.137605 OCCU 0.5 BISO 50.0 ATOM Se XYZ 0.716238 0.238362 0.0869784 OCCU 0.5 BISO 50.0 ATOM Se XYZ 0.259739 0.00855349 0.239787 OCCU 0.5 BISO 50.0 ATOM Se XYZ 0.343637 0.168551 0.319304 OCCU 0.5 BISO 50.0 ATOM Se XYZ 0.173773 -0.0720953 0.391003 OCCU 0.5 BISO 50.0 ATOM Se XYZ 0.179076 0.0804735 0.520765 OCCU 0.5 BISO 50.0 ATOM Se XYZ 0.926494 0.231291 0.18954 OCCU 0.5 BISO 50.0 DNAME PEAK COLUmn F+=F_peak(+) SF+=SIGF_peak(+) F-=F_peak(-) SF-=SIGF_peak(-) FORM Se FP=-4.0 FPP=4.0 DNAME INFL COLUmn F+=F_infl(+) SF+=SIGF_infl(+) F-=F_infl(-) SF-=SIGF_infl(-) FORM Se FP=-6.0 FPP=2.0 ALLIn # phase keyword to make things faster! PHASe eof-bp3 ############################################################## # Example 5 # 3 wavelength MAD + native bp3 HKLIN $CEXAM/tutorial/data/gere_MAD_nat_scaleit1.mtz \ HKLOUT $CCP4_SCR/gere_MAD_phase.mtz << eof-bp3 # MAD data + natve # always define MAD "derivative" crystal first! Xtal DER1 ATOM Se XYZ 0.567606 0.19651 0.117643 OCCU 0.5 BISO 50.0 ATOM Se XYZ 0.637982 0.0428475 0.217668 OCCU 0.5 BISO 50.0 ATOM Se XYZ 0.469871 0.255659 0.23827 OCCU 0.5 BISO 50.0 ATOM Se XYZ 0.49385 0.188126 0.41977 OCCU 0.5 BISO 50.0 ATOM Se XYZ 0.794401 0.401274 0.137605 OCCU 0.5 BISO 50.0 ATOM Se XYZ 0.716238 0.238362 0.0869784 OCCU 0.5 BISO 50.0 ATOM Se XYZ 0.259739 0.00855349 0.239787 OCCU 0.5 BISO 50.0 ATOM Se XYZ 0.343637 0.168551 0.319304 OCCU 0.5 BISO 50.0 ATOM Se XYZ 0.173773 -0.0720953 0.391003 OCCU 0.5 BISO 50.0 ATOM Se XYZ 0.179076 0.0804735 0.520765 OCCU 0.5 BISO 50.0 ATOM Se XYZ 0.926494 0.231291 0.18954 OCCU 0.5 BISO 50.0 DNAME PEAK COLUmn F+=F_peak(+) SF+=SIGF_peak(+) F-=F_peak(-) SF-=SIGF_peak(-) FORM Se FP=-4.0 FPP=4.0 DNAME INFL COLUmn F+=F_infl(+) SF+=SIGF_infl(+) F-=F_infl(-) SF-=SIGF_infl(-) FORM Se FP=-6.0 FPP=2.0 DNAME HRM COLUmn F+=F_hrm(+) SF+=SIGF_hrm(+) F-=F_hrm(-) SF-=SIGF_hrm(-) FORM Se FP=-3.0 FPP=1.0 # This version of BP3 will just ignore the NATIVE in MAD phasing, so you might as well # comment this out! ! Xtal Native ! DNAME native ! COLUMN F=F_native SF=SIGF_native ALLIn # phase keyword to make things faster! PHASe eof-bp3