BP3 Version 1.0 - Documentation

NAME

bp3 - multivariate likelihood substructure refinement and phasing of S/MIR(AS) and/or S/MAD.

SYNOPSIS

bp3 hklin foo.mtz hklout foo_out.mtz

Keyworded input

DESCRIPTION

This program will refine heavy and/or anomalously scattering atomic parameters along with errors parameters to generate phase information.

GETTING STARTED

The best way to start is to use the CCP4i interface or example scripts. The example scripts are straightforward to modify for most possible phasing scenarios and are given at the end of this document. If you would like to determine phases quickly, check out the PHASe keyword.

MAD PHASING

At the moment, S/MIR(AS) and SAD phasing is quite fast - MAD is a bit slow. So, it might be worth starting a first run with the PHASe keyword if you have a MAD experiment.

KEYWORDED INPUT

Note that the ordering of some keywords is important. In particular, the XTAL subkeywords (CELL, ATOM, DNAME) must be preceded by the corresponding XTAL keyword, and similarly for the ATOM and DNAME subkeywords.

SITE <NUMB> <Xfrac> <Yfrac> <Zfrac> [NOREf [X] [Y] [Z] ]

The SITE keyword should be used if you have the same site in more than one crystal. The SITE keyword can not be used in combination with the FRAC subkeyword of ATOM (described below).

<NUMB>

The Site number - the first site number must be 1 and incremented by 1 with every other SITE keyword.

<Xfrac> <Yfrac> <Zfrac>

Fractional atomic coordinates for the SITE.

NOREF X Y Z

The NOREf subkeyword indicates that the X, Y and/or Z coordinates of this site will not be refined. Default: refine all the coordinates.

XTAL <ID>

<ID>

The crystal's name/identification string.

XTAL SUBKEYWORDS:

CELL

<a> <b> <c> <alpha> <beta> <gamma>

<a> <b> <c> <alpha> <beta> <gamma>

Cell parameters for the given XTAL. Default: take the values from the mtz file.

MODL <pdbfile>

<pdbfile>

Input a pdb file containing substructure coordinates in standard pdb form. Note! only input coordinates with MODL or XYZ or SITE. Using any two of the keywords will result in an error.

The format of a line of a pdb file should be the following:

HETATM    1  SE  HAT     1      25.284  28.195  17.180  1.00 33.96

OR

ATOM      1  SE  HAT     1      25.284  28.195  17.180  1.00 33.96

The fixed format for the columns agree with the pdb format, but column 3 has to be the name of your substructure that matches an atom in $CLIBD/atomsf.lib. See file gere.pdb in the examples sub-directory for an example.

ATOM <ID> [SITE <NUMB> ]

<ID>

The atom's name. The name must match a (case insensitive) atom's name in $CLIBD/atomsf.lib.

[SITE <NUMB> ] If sites are specified with the SITE keyword, give this keyword along with the corresponding site number for this atom.

ATOM SUBKEYWORDS:

XYZ <Xfrac> <Yfrac> <Zfrac> [NOREf [X] [Y] [Z] ]

<Xfrac> <Yfrac> <Zfrac>

Fractional atomic coordinates.

NOREF X Y Z

Including the NOREf subkeyword of XYZ indicates that the X, Y and/or Z coordinate of this atom will not be refined. Default: refine all the coordinates.

Note! The FRAC keyword can not be used in combination with the SITE keyword.

OCCU <occ> [NOREf]

<occ>

Atomic occupancy - at the moment, convergence is faster if you start with a lower value (ie. 0.25)

NOREf

The atomic occupancy will not be refined

BISO <bfac> [NOREf]

<bfac>

Atomic isotropic B factor. For faster convergence, use the B-factor from a Wilson plot (ie. from the WILSON program). This will be the default value when using CCP4i.

NOREf

The atomic B factor will not be refined

UANO <U11> <U12> <U13> <U22> <U23> <U33> [NOREf]

<U11> <U12> <U13> <U22> <U23> <U33>

Atomic anisotropic U factor. If only one value is given (ie. <U11>), it will be assumed that it was an Atomic isotropic B factor, and it will be converted to an anisotropic U.

NOREf

The anisotropic U's will not be refined.

DNAMe <ID>

The dataset identifier. This keyword is required.

DNAMe SUBKEYWORDS:

COLUmn F=<f> SF=<sf> F+=<f+> SF+=<sf+> F-=<f-> SF-=<sf->

Diffraction data for the XTAL and DNAMe defined. If anomalous data is not to be used, set F and SF only. If using anomalous data, set F+, SF+, F-, SF-. Setting both F and F+ will result in an error. If only F and DANO is present in the mtz file, use the ccp4 program mtzMADmod to change F/DANO to F+/F-.

<f>

|F| (observed structure factor amplitude *if no anomalous data is present*).

<sf>

Corresponding sigma for <f>.

<f+>

|F+| (observed structure factor amplitude of positive Bijvoet pair).

<sf+>

Corresponding sigma of <f+>.

<f->

|F-| (observed structure factor amplitude of negative Bijvoet pair).

<sf->

Corresponding sigma of <f->.

FORM <ATOMID> [FP <fp>] [FPP <fpp>]

Specify f' and f'' values - the default is to use CuKa radiation. <ATOMID> MUST match an atom previously declared by the ATOM keyword.

RESO <hires> <lores>

Specify resolution limits for the given XTAL and DNAMe diffraction data. Default: use all the data available in the mtz file.

BINS

Number of bins for luzzati parameter estimation and refinement and output of statistics.

ISOE <isoe1> <isoe2> ... <isoen> [NOREf]

Luzzati isomorphic error parameters. The number of parameters MUST be the same as the number of BINS, or an error will result. If the NOREf keyword is given, the parameters will not be refined.

ANOE <anoe1> <anoe2> ... <anoen> [NOREf]

Luzzati anomalous error parameters. The number of parameters MUST be the same as the number of BINS, or an error will result. If the NOREf keyword is given, the parameters will not be refined.

SDLU <sdlu1> <sdlu2> ... <sdlun> [NOREf]

Luzzati error parameters in SAD function. The number of parameters MUST be the same as the number of BINS, or an error will result. If the NOREf keyword is given, the parameters will not be refined.

KSCALe <k> [REFIne]

Scale factor to apply to the data set to scale it relative to the reference set. The default is 1 and not to refine this parameter, as it is highly correlated to the Luzzati isomorphism parameter.

BSCALe <b> [REFIne]

Isotropic B-factor to apply to the data set to scale it relative to the reference set. The default is 0 and not to refine, as again, it is highly correlated to the Luzzati isomorphism parameter.

OPTIONAL KEYWORDS:

REFIne

The program will refine atomic and error parameters and calculates phases (default).

PHASe

The program will just calculate phases with refining only atomic occupancies in the first macro-cycle, refining occupancies and error parameters in the second macro-cycle and then occupancies, coordinates and error parameters in the second and last macro-cycle. The keyword specifies the micro-cycles within a macrocycle - the default is 2. Use should use this option for very quick phasing, but make sure the occupancies and coordinates inputted are from CRUNCH2 or SHELXD and the B factors are also reasonable (ie. a good guess is the Wilson B factor for the data set). The occupancies should be normalized to be between 0 and 1.

CYCle

The number of cycles of refinement to perform (unless convergence is reached before) Default: 500

NORM

The minimum magnitude of the gradient vector required for convergence/termination of minimization. Default: 25

WOLFe <alpha> <beta>

alpha and beta parameters for the Wolfe (or Amijo/Goldstein) line search conditions. Default: alpha = 0.0001, beta = 0.975

REFAll

For greater numerical stability, the program by default refines just the occupancies in the first refinement cycle and then all parameters (error and atomic) in the second and final. This keyword goes directly to refining all parameters without refining occupancies and should be used in subsequent refinements using refined values of the error and atomic coordinates.

OUTPut <outputname>

<outputname> is the string associated with the pdb file, crank XML and script file that bp3 writes out.. The default <outputname> is "heavy".

NODEs [CENTric <cen> PHASe <pha> AMPLitude <amp> SAD <sad> ]

Increase the number of nodes (i.e. points of evaluation for numerical integration) for the CENTric integral and the acentric PHASe and AMPLitude integral. Default: CENTRic = 5, PHASe = 25, AMPLitude = 5, SAD = 30.

THREshold

Parameter giving value of FOBSref/SIGFref (i.e. f over sigma for the reference data set) of when to switch from one dimensional numerical integration to two dimensional integration for acentric reflections. Therefore, if THREshold is less than or equal to ZERO, only one dimensional (phase) integration will be performed. Or, if THREshold is very large (i.e. 100000), a two dimensional integration (both amplitude and phase) will be done. Default: 4.

ACENtric

Only refine and phase acentric reflections. For testing purposes only.

CENTric

Only refine and phase centric reflections. Possibly useful, but not recommended.

TITLe <title>

Title to be added to the mtz file. Default: "Phasing from BP3".

VERBose <n>

Specify amount of information to be outputted (where n is a positive integer). n = 0 is the normal output, n = 1 is more output and n = 2 is for debugging purposes. Default: n = 0.

OUTPUT:

COLUMNS in HKLOUT

FPHASED

Structure factor amplitude of reference data set

SIGFPHASED

Corresponding sigma of FPHASED

FB

Maximum likelihood amplitude (roughly equal to FOM * FP)

PHIB

Maximum likelihood phase

PHIBOH

Maximum likelihood phase for the enantiomorph/other hand (PHIBOH = -PHIB)

FOM

Figure of merit.

HLA, HLB, HLC, HLD

Hendrickson-Lattman coefficients

PDB FILES:

Orthogonal heavy atom parameters in file <outputname><crystalnumber>.pdb

CRANK XML FILES:

CRANK XML file for any subsequent jobs in file <outputname><crystalnumber>.xml

BP3 script FILES:

in file <outputname>.sh

EXAMPLES

Example (1)

#!/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

##############################################################

Example 2 - SAD Phasing

#!/bin/sh

set -e

bp3 HKLIN $CEXAM/tutorial/data/gere_MAD.mtz \
    HKLOUT $CCP4_SCR/gere_MAD_phase.mtz << eof-bp3

# selenium

Xtal DER1
  ATOM Se
    XYZ 0.567606  0.19651  0.117643
    OCCU 0.5
    BISO 25.0
  ATOM Se
    XYZ 0.637982  0.0428475  0.217668
    OCCU 0.5
    BISO 25.0
  ATOM Se
    XYZ 0.469871  0.255659  0.23827
    OCCU 0.5
    BISO 25.0
  ATOM Se
    XYZ 0.49385  0.188126  0.41977
    OCCU 0.5
    BISO 25.0
  ATOM Se
    XYZ 0.794401  0.401274  0.137605
    OCCU 0.5
    BISO 25.0
  ATOM Se
    XYZ 0.716238  0.238362  0.0869784
    OCCU 0.5
    BISO 25.0
  ATOM Se
    XYZ 0.259739  0.00855349  0.239787
    OCCU 0.5
    BISO 25.0
  ATOM Se
    XYZ 0.343637  0.168551  0.319304
    OCCU 0.5
    BISO 25.0
  ATOM Se
    XYZ 0.173773  -0.0720953  0.391003
    OCCU 0.5
    BISO 25.0
  ATOM Se
    XYZ 0.179076  0.0804735  0.520765
    OCCU 0.5
    BISO 25.0
  ATOM Se
    XYZ 0.926494  0.231291  0.18954
    OCCU 0.5
 DNAME PEAK
   COLUmn F+=F(+)SEpeak SF+=SIGF(+)SEpeak F-=F(-)SEpeak SF-=SIGF(-)SEpeak
   FORM Se FP=-4.0 FPP=4.0

ALLIn

eof-bp3

##############################################################

Example 3

#!/bin/sh

set -e

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

# Example 4

# 2 wavelength MAD

#!/bin/sh

set -e

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

# Example 5

# 3 wavelength MAD + native

#!/bin/sh

set -e

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

Last modified: Tue Dec 6 21:14:39 CET 2005