Xsight

Contents

Release March 2000

1. Introduction

Xsight structure

Getting started

Note on command names

About this guide

Xsight online help

2. Theory

Phase determination

Overview of the phase problem

Isomorphous replacement

MAD phase determination

Phasing steps

Scale determination between datasets

Determination of sites for heavy atoms and anomalous scatterers

The difference Patterson function

Interpretation of the difference Patterson function

Location of additional sites

Refinement of heavy atom and anomalous scatterers

Calculation of protein phases

Molecule 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

The R factor and the correlation coefficient

Calculation of structure factors

Patterson correlation translation function

Electron density correlation translation function

Phase relationship among symmetry-related structure factors

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

The random tweak method

Monte Carlo loop search

Refinement of loop conformation by Monte Carlo techniques

The random tweak method for loop generation

Monte Carlo driver

3. Implementation

Crystals and projects

4. Methodology

Getting started

Importing structure factor data

File formats used by the Xsight module

The Fin file format

The Phase file format

Data files for the CNX program

Converting a reflection datafile 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

Molecule 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

Defining the non-crystallographic symmetry relations

Setting up the protein subunit envelope

Running the non-crystallographic symmetry averaging

Model fitting: Xfit

Viewing models and electron density maps

Graphics handling

Colors

Plotting

Vu objects

Model fitting: waters

Obtaining a difference map

Automatic location of water molecules

Checking the water sites

Refinement

Simulated annealing

Setting up files for refinement with the CNX program

Running refinement calculations with the CNX program

Single rigid-body refinement

Setting up a rigid-body refinement

Multiple rigid-body refinement

Least-squares minimization

Selecting reflection data for the refinement

Selecting a refinement strategy

Changing the stereochemical restraints

Running the refinement

Setting up stereochemical dictionaries for new ligands

Checking the stereochemical quality of a structure

Visualization of crystal symmetry

Crystal packing diagrams

Analyzing the atomic interactions between molecules

5. Tutorial

Overview of tutorial lessons

Hardcopy tutorial lessons

Setting up to run tutorials

Isomorphous replacement

Merging native and derivative data 120

Finding heavy-atom sites for the first derivative 127

Adding a second derivative 136

Phase determination from MAD data

MAD phase determination 147

Density modification

Solvent flattening and histogram matching 171

Non-crystallographic symmetry averaging 180

Density fitting

Making maps and basic fitting techniques 193

De novo map fitting 206

Molecule replacement

Calculating a self-rotation function 220

Generating structure factors for the search model 232

Ordinary cross-rotation function 237

Translation search 243

Applying the solutions 255

Refinement

Rigid-body refinement 260

Multi-rigid-body refinement 267

Simulated annealing refinement 276

Least-squares minimization 287

Completing the atomic model

Generating ligand dictionaries 294

Locating ordered water molecules 299

Visualization

Richardson diagrams 306

Display of atomic models with electron density maps 311

Display and creation of symmetry-related molecules 317

APPENDICES

A. References

B. Insight II Commands

Xsight module

Utilities pulldown

Utilities/Crystal

Utilities/Project

Utilities/View_PostScript

Utilities/Display_Density

Data_Control pulldown

Data_Control/Import_Data

Data_Control/Display_Recip_Space

Data_Control/Data_Processing

MAD pulldown

MAD/Combine_MAD_Data

MAD/Calc_Anom_Diff

MAD/Determine_Phases

MAD/Calc_Absolute_Scatt

MAD/Refine_Anom_Sites

MIR pulldown

MIR/Merge_Data

MIR/Calc_Fourier

MIR/Contour_Map_3D

MIR/Find_Heavy_Atoms

MIR/Calc_Phases

MIR/Merge_Phases

MIR/Predict_Patterson

MIR/Contour_Map

MIR/Statistics

Mol_Replacement pulldown

Mol_Replacement/Search_Model

Mol_Replacement/Rotation_Func

Mol_Replacement/Translation_Func

Mol_Replacement/Apply_Transform

Mol_Replacement/MR_Tools

Modify_Density pulldown

Modify_Density/Auto_Density_Mask

Modify_Density/Edit_Density_Mask

Modify_Density/Apply_Density_Mask

Modify_Density/Set_NonCryst_Symm

Modify_Density/Set_Subunit_Mask

Modify_Density/Average_NCS_Density

Model_Building pulldown

Model_Building/Density_Fitting

Model_Building/Molecule_Update

Model_Building/Skeletonization

Model_Building/Waters

Refinement pulldown

Refinement/Setup_CNX

Refinement/SA_Refine

Refinement/Multi_Body_Refine

Refinement/B_Factor_Refine

Refinement/Rigid_Body_Refine

Refinement/Minimize

Refinement/Dictionary

ProStat pulldown

ProStat/Statistics

ProStat/Struct_Check

ProStat/Residue_Dihedral

ProStat/SecondaryClassify

ProStat/Access_Surf

Symmetry pulldown

Symmetry/Packing

Symmetry/Contacts

Symmetry/Merge_Molecule

C. XtalView Commands

Xcontur program

Main menu

Supplemental menus

File menu

Print menu

View menu

Labels menu

Defaults menu

Xedh program

Files menu

Electron Density Histogram window

Xfft program

Defaults menu

Xfit program

Mouse behavior

Keyboard shortcuts

Floating menu bar

Default MB3 pop-up menu

Expert MB3 menu

Center at Pick (Expert menu)

Fit (Expert menu)

Middle Button Mode (Expert menu)

Clear labels/contacts (Expert menu)

Contour (Expert menu)

Geometry Refine (Expert menu)

Real-Space Refine (Expert menu)

Model (Expert menu)

Rotate View 90 (Expert menu)

Save Model Being Fit (Expert menu)

Symmetry Atoms (Expert menu)

Slab View (Expert menu)

Misc Controls (Expert menu)

Ridge Lines (Expert menu)

Clear Stack (Expert menu)

Expand Top 2 on Stack (Expert menu)

Toggle Stereo (Expert menu)

Swap Menu (Expert menu)

Main Xfit menu

Xfit supplemental menus

Files menu

Ridgelines menu

LSQ Fit menu

View menu

Show menu

Colors menu

FFT menu

Refine menu

Control menu

Contours menu

Model menu

SFCalc menu

Labels menu

Xheavy program

Xheavy Edit menu

Xhercules program

Xmerge program

Xmergephs program

Xpatpred program

Xprepfin program

Xprolsqtool program

Main menu

Reflection Limits menu

Refinement Parameters menu

Xrspace program

Xresflt program

Xskel program

Xstat program

D. 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

BTOC-relationship--(B2CANG(i), i = 1, 3), B2CCON*1

CELL-parameters--(CELL(i, 3), i = 1, 6)

FOBS-file--OBSFIC*72

FORMat--OBSFMC*72

POWEr--CPOWER

REJEction-criteria--CSGCUT, CCUTLO, CCUTHI

SYMMetry

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

BOverall -- BOVRAL

BZero -- BZERO

INput -- CORINP*72

OUtput -- COROUT*70

GROUp

P1PC-refinement

Locked translation function

GLTFunction

CUTOff -- GLTFCT

DIREct-summation -- QDRECT

MAPFile -- LTFMAP*72

OVERlap -- NOVLP, DCUTTF

PACKing-check -- QPACK

RADIus -- RADMAX

RFPEak -- NTFPKS

SLIMits -- I, BEGIN, END, INCREMENT

Miscellaneous commands

ANGLe

LOCAsu

LOCFit

LOCRotate

MATRix

SYMShow

Electron density rotation translation function

RSRF

TFUNction

Contour plots

CNTFile

CNTLevel

CNTSection

Storage limits

E. 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

ADd-residue-number -- N

APpend -- N

BIncrement -- BINCRM

BOverall -- BOVRAL

BZero -- BZERO

CEnter -- (CENTER(i), i=1, 3)

CHain -- chnnam*1

COpy -- M, N

FCalc -- CALFIL*72, CALFMT*40

FLag -- CORFLG*1

FOrmat -- FMTTYP*1, CORFMT*40

INput -- CORFIL*72

OUtput -- OUTFIL*70

PErmute -- L, M, N

REtrieve -- N

ROtate -- (ROTANG(i), i=1, 3), ANGTYP*1, (ROTCEN(i), i=1, 3)

SAlt-bridge -- DSALT

SIze -- RADIUS

STore -- N

SWap - M,N

TRanslate -- (VECTOR(i), i=1, 3)

TYpe -- CORTYP*2

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

CONTact --

CUTOff -- CUTOFF

DCUToff -- DCACUT, NCACUT, NCAMOD

ECEC --

EOEC -- (MOLCUL(i), i=1, NSYM)

F1F1

F2F2

FOFC

HAND--QHAND

IOIC

PACKing-calculation

PHASe-only

POPC -- (MOLCUL(i), i=1, NSYM)

RFCEnter--X,Y,Z

RFFIle -- RFFILE*72

RFMAp -- RFCUT, NRFPK

RFPEak

RFPC

RFSAve -- NRPK,QSVALL

RFSOrt -- NRFSRT

SELF-vector-removal -- SELFWT

SFCAlculation -- OBSNEW*72

SHELl -- NSHELL

MAPFile

PEAK-Cutoff

RESOlution-limits

SECTion

SIZE

SLIMits

Contour plots

CNTFile

CNTLevel

CNTRegion

CNTSection

Storage limits

F. MADSYS Keywords

Program flow

Keywords

Function keywords and input requirements

ABSOLUTE

ANOMERGE

ANORES

ANOSCL

ASLSQ

F2ANO

FA

MADABCD

MADFAZ

MADLSQ

MERGIT

PHASE

WVLSCL

Index