#!/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