Xsight

Contents

Release 98.0, December 1998

1. Introduction

Xsight structure

Getting started

Note on command names

About this manual

Xsight online help

2. Theory

Phase determination

Overview of the phase problem

Scale determination between data sets

Determination of sites for heavy atoms and anomalous scatterers

Refinement of heavy atom and anomalous scatters

Calculation of protein phases

Molecular replacement

Introduction to the rotation function

Slow rotation function

Fast rotation function

Ordinary self-rotation function

Ordinary cross-rotation function

Locked self-rotation function

Locked cross-rotation function

General strategies for rotation function calculations

Specialized translation functions

Cross-locked rotation function

Real space rotation function

Location of a local symmetry axis

Positions related by local symmetry

Introduction to the translation function

Density modification

Basic principles

Solvent flattening algorithms

Histogram matching algorithms

Non-crystallographic symmetry averaging algorithms

Structure refinement

Basic principles

Simulated annealing

Bulk solvent scattering correction

Least-squares minimization with ProLSQ95

Loops

Monte Carlo loop generation and fitting

Refinement of loop conformation by Monte Carlo techniques

3. Implementation

Crystals and projects

4. Methodology

Getting started

Importing structure factor data

File formats used by the Xsight module

Converting a reflection data file to the Xsight file
formats

Phase determination by Multiple Wavelength Anomalous Diffraction (MAD)

Determining the expected scattering

Combining and scaling of the MAD data sets

Determination of anomalous scattering from the experimental data

Phase determination

Refinement of parameters for the anomalous scatterers

Phase determination by isomorphous replacement

Scaling and merging native and derivative data sets

Calculation of difference Patterson functions

Examining difference Patterson maps

Automatic location of heavy atom sites

Refinement of heavy atom sites and phase
determination

Molecular replacement

Self-rotation function

Structure factor calculations

Cross-rotation function

Translation function

Locked rotation function

Fast rotation function

Refinement of rotation function solutions

Map contouring

Visualization of rotation and translation functions

Generating the structure solution

Density modification

Determining a protein mask

Checking and editing a protein mask

Solvent flattening and histogram matching

Non-crystallographic symmetry

Model fitting: Xfit

Viewing models and electron density maps

Graphics handling

Model fitting: waters

Obtaining a difference map

Automatic location of water molecules

Checking the water sites

Refinement

Simulated annealing

Single rigid-body refinement

Multiple rigid-body refinement

Least-squares minimization

Setting up stereochemical dictionaries for new ligands

Checking the stereochemical quality of a structure

Visualization of crystal symmetry

5. Tutorial

Overview of tutorial lessons

Hardcopy tutorial lessons

Setting up to run tutorials

Isomorphous replacement

Merging native and derivative data

Finding heavy atom sites for the first derivative

Adding a second derivative

Phase determination from MAD data

MAD phase determination

Density modification

Solvent flattening and histogram matching

Non-crystallographic symmetry averaging

Density fitting

Making maps and basic fitting techniques

De novo map fitting

Molecular replacement

Calculating a self-rotation function

Generating structure factors for the search model

Ordinary cross-rotation function

Translation search

Applying the solutions

Refinement

Rigid-body refinement

Multi-rigid-body refinement

Simulated annealing refinement

Least-squares minimization

Completing the atomic model

Generating ligand dictionaries

Locating ordered water molecules

Visualization

Richardson diagrams

Display of atomic models with electron density maps

Display and creation of symmetry related molecules

A. References

B. Insight II Commands

Xsight module

Utilities pulldown

Data_Control pulldown

MAD pulldown

MIR pulldown

Mol_Replacement pulldown

Modify_Density pulldown

Model_Building pulldown

Refinement pulldown

ProStat pulldown

Symmetry pulldown

C. XtalView Commands

Xcontur program

Main menu

Supplemental menus

Xedh program

Files menu

Electron Density Histogram window

Xfft program

Xfit program

Mouse behavior

Keyboard shortcuts

Floating menu bar

Default MB3 pop-up menu

Expert MB3 pop-up menu

Main Xfit menu

Xfit supplemental menus

Xheavy program

Xheavy Edit pop-up menu

Xhercules program

Xmerge program

Xmergephs program

Xpatpred program

Xprepfin program

Xprolsqtool program

Main menu

Xrspace program

Xresflt program

Xskel program

Xstat program

D. New XtalView Features

E. REPLACE Rotation Function (GLRF) Keywords

General input commands

COMMent

PRINt-File

STOP

TITLe

Conventions

EULEr-Angle

POLAr-Angle

ORTHogonalization

Specification of local symmetry

LOCSymmetry

LOCexpand

LOCInterpolate

LOCOrient

LOCUpdate

Commands that define the first (A) crystal

ACELL-Parameters

ASYMmetry

AOBS-File

AFORmat

ACUT-off

APOWer

NSHEll

ORIGIN-Removal

Commands that define the second (B) crystal

CUTOff

Commands that define the third (C) crystal

CXTAl

Specification of search parameters

BOXSize

CROSs-search

GEVAluation

MAPFile

OANGle

PEak-Cutoff

PKFIt

PRERotation

RADIus

RCUToff

RESOlution-limits

SANGle

SECTion

SELF-search

SLIMits

XCORrelate

Fast rotation function

FAST-rotation-function

NORMalize

Patterson correlation refinement

COORdinate

GROUp

P1PC-refinement

Locked translation function

GLTFunction

Miscellaneous commands

ANGLe

LOCAsu

LOCFit

LOCRotate

MATRix

SYMShow

Electron density rotation translation function

RSRF

TFUNction

Contour plots

CNTFile

CNTLevel

CNTSection

Storage limits

F. REPLACE Translation Function (TF) Keywords

General input commands

COMMent

*PRINt-File

*STOP

*TITLe

Conventions

*EULEr-Angle

*POLAr-Angle

*ORTHogonalization

Commands that define the search atomic model

*MODEl-cell

*COORdinate

Commands that define the crystal

*CELL-Parameters

SYMMetry

LATTice-type

FOBS-File

FORMat

FREJection

POWEr

Structure factor calculation

ATOM-type

DIREct-summation

TABLe-lookup

Specification of search parameters

FUNCtion

MAPFile

PEAK-Cutoff

RESOlution-limits

SECTion

SIZE

SLIMits

Contour plots

CNTFile

CNTLevel

CNTRegion

CNTSection

Storage limits

G. MADSYS Keywords

Program flow

Keywords

Function keywords & input requirements