CNX 2000

Release March 2000

Contents

1. Overview

General enhancements

New features for X-ray crystal structure determination

New features for NMR structure determination

CNX source code and release tree

CNX program

CNX release tree

2. Methodology

General enhancements

ABNR energy minimization routine

Background

Implementation

Improved data and structure handling

Data model extensions

Structure files (PSF and MTF file formats)

Reading structure data

Writing structure files

MTF data items

Creating molecule structures using the segment builder

Reading PDB and mmCIF files, and automatic discrete disorder

Writing coordinate files

Automatic discrete disorder

Symmetric and asymmetric atom interactions

Reflection data

Control statements

Atom selection

Vector commands

Topology

Plot files

X-ray crystallographic refinement

Torsion angle dynamics for structure refinement

Background

Implementation

Maximum-likelihood targets for structure refinement

Background

Implementation

Andersen thermal coupling

Background

Implementation

Bulk-solvent scattering correction

Background

Implementation

Probabilistic multi-wavelength anomalous dispersion (MAD) phasing

Background

Implementation

Tutorial

Data conversion

Background

Implementation

NMR structure determination

Torsion-angle dynamics for NMR structure determination

Background

Implementation

Structure determination using ambiguous restraints

Introduction

Overview

CNX/ARIA commands

J coupling and proton and ¹³C chemical shift NMR refinement

Direct coupling constant refinement

Direct secondary carbon chemical-shift refinement

Direct ¹H chemical-shift refinement

Fast refinement using direct NOEs

Background

Implementation

Structure refinement using additional angular information

Structure refinement using cross-correlated dipole-dipole relaxation rates

Structure refinement using residual dipolar couplings

APPENDICES

A. References

B. Command Reference

X-PLOR/Xrefine commands not used in CNX/Xray

CNX/XRay commands

CNX/XRAY command and syntax overview

IMF

SMF

LIDENS

MAPYARD

SKELETONIZE

SYMMETRY

SCATTER

REFLECTION

DECLARE, REFLECTION DECLARE

UNDECLARE

RENAME

GROUP, REFLECTION GROUP

UNGROUP

REFLECTION INDEX

QUERY

DELETE

MULTISCALE, SCALE

ASSOCIATE

PREDICT

WRITE REFLECTION

WRITE MAP

READ MAP

FMAP

AVERAGE

GROUP

MANIPULATE

FFT

MASK commands

MASK

WRITE MASK

READ MASK

PROXIMITY

OPTIMIZE commands

OPTIMIZE OVERALL

OPTIMIZE GROUP

OPTIMIZE BFACTOR

SPECIAL

SEARCH commands

SEARCH ROTATION

SEARCH CLUSTER

SEARCH TSMAP

SEARCH DIRECT

PSEARCH

PEAKPICK

STATISTICS

DO

SHOW

HISTOGRAM

GENERATE

List of Tables

Index