QUANTA 2006 <BR> X-Ray Structure and Analysis

QUANTA 2006
X-Ray Structure and Analysis

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How to Use This Book

How to find information
Typographical conventions

1. Introduction to X-Ray Structure Analysis and Refinement

   Accelrys' X-Ray crystallography applications
      X-POWERFIT
      X-AUTOFIT
      X-BUILD
      3D notebook and other tools
      CNX
      X-SOLVATE
      X-LIGAND
   The crystallographic structure determination process
      Before you begin
      Collect and process data
      Determine phases
      Generate initial model
      Build and refine model
      Refinement
      Adding ligands
      Add solvent and refine final model
      Assess model

2. Using the X-applications

   Introduction
   Application subdivision
   Electron density Bones
      Mask generation
   Ca tracing
      Adding Ca trace atoms.
      Moving Ca trace atoms
      Moving Ca-trace segments
      Ca trace polarity
   Sequence assignment
      Loading sequences
      Sequence assignment
      Unique sequence
   Ca-trace -> all atom model
      Chain polarity
      Where do the coordinates go?
   Model building
      Refinement
      Grid refinement
      Gradient refinement
      Monte Carlo refinement
      Geometry refinement
      Model building protein/NA
      Model build ligands and waters
      General comments
      Validation

3. Managing Maps

   Interactive Map generation
      Typical Use
   Maps Management table
      Menu bar
      Maps menu
         Import
         Add a Map
         Delete a Map
         Replace a Map
         List Maps
         Hide Table
      Contour menu
         Contour Maps
         Contour Mode
         Characteristics of Display Lines
         Define Contour Levels
      Utils menu
         Purge Contours
         Reset Drawing
      Edit line
      Column headings
      Rows
   Managing maps in various QUANTA applications
      X-LIGAND, X-SOLVATE:
      X-POWERFIT, X-AUTOFIT:X-BUILD:

4. Introduction to X-AUTOFIT/X-BUILD/X-POWERFIT (X-FIT)

   Map generation
   Map contouring
   Density skeletonization
   Solvent masks
   3D text editor
   Automated Ca tracing
   Ca tracing
   Automated sequence assignment and fuzzy logic assignment
   Ca trace --> all-atom model
   Model building
   Refinement techniques
   Validation techniques
   Data logging
   Data integrity
   X-AUTOFIT in QUANTA
   Memory requirements for X-AUTOFIT
   Accessing X-AUTOFIT
   General X-AUTOFIT and X-BUILD behavior
      Using multiple structures and maps in X-AUTOFIT
      Palettes and tool activity in X-AUTOFIT
      Dial box
      Graph windows
      Tables

5. Using X-AUTOFIT

   Solvent boundaries or map masks
      Parameterization
      Editing bones
      Generating a mask
      Editing masks
      Summary
   Bones
      Displaying and skeletonizing an electron density map
      Determining map quality
         To get information about map quality
         Improving map quality
      Modifying the skeletonization initial cut-off parameter
         To adjust the Start parameter
         Adjusting branch trimming parameters
         To adjust branch parameters
      Using bones with masks
         Deleting bones points
         To delete bones points
         To change the strand type
      Bones and symmetry
      Using bones with Ca-tracing
   Ca-tracing
      Generating Ca segments using assisted carbon building
         To generate a new segment
      Editing segment and Ca atoms
         Using the pseudo-Ramachandran plot
         Positioning the next Ca atom
      Evaluating and changing segment polarity
         To evaluate segment polarity
         To change segment polarity
      Cut/paste Ca segments
         To join two segments
         Cutting segments
      Templates and rigid body editing of Ca traces
   Sequence assignment
      Reading in sequence information
      Fitting a sequence to a segment
         Generating sequence alignment information
         Redefining the weights
         Creating new definitions
      Finding unique sequences
      Predicting secondary structure
   Building all-atom representation from Ca trace
         Which builder to use
         How to build
      Building main chain coordinates by RSR
      Building mainchain coordinates by database fragment fitting
      Building the mainchain coordinates by Ca direct correlation
      Building the sidechain coordinates by RSR
      Building sidechains by modeling.
      Automated rebuilding in X-BUILD
   References

6. Using X-BUILD

   Protein or nucleic acids
      Proteins
      DNA/RNA
      Nomenclature
      Hydrogen modes
   Controlling the display
      Extent of display
      The current residue value
      Modal and amodal/active residue mode
      Placement of the view
         By coordinates
         By bones
         By atom
         Along sequence
         Graph plots
         Placement by Validation graph.
         Placement by Validation Table.
         Placement by Last Command table.
         By text markers
      Graph plots
         Ramachandran plots
         DNA/RNA circle plot
   Picking screen information
   Symmetry
   Interface to run external programs
   Advanced validation techniques
      Table data
      Picking data
      Table contents
         Table 1 (atom table)
         Table 2 (residue table)
         General table
         Scratch table
      Fixed size of atom and residue tables
      Inconsistent data
   Graphs and plotting
         Table names
         X data
         Legends/annotation
         Add/deleting annotations
         Hardcopy plotting
   Last commands
         The table contents
         Picking title entries in the table
         Picking cell entries
   X-BUILD features
      RSR vs. gradient body refinement
      RSR vs. Move atom and RSR
      Defining torsion angles for unknown residues
      Missing or incorrect atoms
      Regularization
      Regularization compared to RSR
      Regularization and disulfides
      Hydrogen representations
      Disorder
      Clamping of alternate conformations
      C-terminal oxygen atoms in proteins
      5´ Terminal residues in nucleic acids
   Summary of using X-BUILD
      Editing each residue
      Waters
      Color
      Manual editing
      Loops
      Structure refinement

7. Using X-POWERFIT

   Introduction
   Data
   Who can use this application?
   Map quality
   Reduced representation (low resolution tracing only)
   Before starting
      Maps
      Masks
      Bones
   The bones parameterization
      Start parameter
   Applying a map mask
   Tracing high resolution structures
      Pathway analysis
      Fragment analysis
      Generation of Ca trace
   Tracing low resolution structures
   Determining the secondary structure in the molecule
      Introduction
      Pattern recognition
      Cluster analysis
      Sheet structure
      Refinement
      Overlap analysis
   Placing the initial Ca atoms
   Automatic generation of the Ca trace
      Start point for tracing
      Pathway analysis
   Consensus tracing
   Adding secondary structure elements
   Adding more secondary structure
   Searching the PDB for similar motif patterns
   Building general structure
   Checking the trace for knots
   Ca refinement
   Generation of all atom models

8. X-AUTOFIT:X-BUILD Tools

   Overview
   Requirements
      Ligands
      Rotatable bonds
         Edited rotatable bonds
         MSF file requirements
      Symmetry
   General use
      Active site searching
      Conformation searching
      Precision
      Refinement
      Masked tools
   X-LIGAND palette
      Search for ligands
      Adjust site volume
      Change search setting...
      Search threshold
      Conf search mode
      Electron density truncation
      Non-bonding
      Partial bond torsion search
      Use 3rd moments
      Z-weights
      Regularize
      Grid search parameters / Max conf to search
      Max time for search
      Intra-ligand Non-bonding
      Grid search parameters / Max tors to search
      Radii / Map display radius
      Radii / Calculation radius
      Position search centre
      Map on/off
      Reset Ligand
      Next site
      Previous site
      Goto site
      Search conformations
      ...Refine all
      ...next conformation
      ...previous conformation
      ...all 20 conformations
      ...Fix search origin
      ...Fix ligand atoms
      ...Clear fixed atoms
      ...fit in stages
      Flip tor 180
      Set active torsions
      Add/del 1 torsion
      Edit torsions
      Edit position
      Refine
      Score fit
      Save ligand to MSF
      Select new ligand
      Database/list
      Exit

10. Using X-SOLVATE

   Molecular coordinates used by X-SOLVATE
   Saving water molecules on exit from X-SOLVATE
   Accessing X-SOLVATE
      Before you begin
      To begin X-SOLVATE
   Using X-SOLVATE
      Searching for water molecules
      To run a search
      Adjusting water molecule position
      Saving the water to MSF
   Search for peaks palette
      Search for waters
      Change search setting...
      Position search center
      Map on/off
      Previous peak
      Next peak
      Goto peak
      Save as water
      Delete water
      Save all peaks
      Exit
      Quit
   Peak search parameters dialog box
      Min density level
      Min distance to protein
      Max distance to protein
      Min sep between peaks
      Calculation radius
      Display radius of map
      Temperature factor

11. Using the CNX Interface

   The CNX Interface palette
   Palette tools
      Set Symmetry
      Set-up Structure Factors
      Parameter Set
      Map Generation
      Rigid Body Refinement
      Refine Structure
      Other CNX Interface tools
      Handling disorder in QUANTA and the CNX interface

12. Setting Up Molecular Systems for CNX

      This chapter describes
      Before you begin
   Setting up a CNX system for a simple protein
      Setting up the structure for CNX
      Running a CNX job to minimize the system
      Running standalone CNX
      Dealing with possible problems
         If CNX does not run or cannot be found
         Seeing the attached-atoms error message
         Unable to generate a PSF because of unknown atom types
      Setting up a system for a nucleic acid, solvent, ion, and ligand
      Doing initial setup
      Preparing the other molecules
      Setting up the CNX calculation

13. Tutorial

   Setup for the tutorial
   Lesson 1: Getting Started with QUANTA
   Lesson 2: Getting Started with the X-Ray Modules
   Lesson 3: Manual CA-tracing
      References
   Lesson 4: Automated CA-tracing
      References
   Lesson 5: Sequence assignment
      References
   Lesson 6: Model Building and Real Space Refinement using X-BUILD
      References
   Lesson 7: Ligand Fitting using X-LIGAND
      References
   Lesson 8: Water Fitting Using X-SOLVATE

A. References

B. Creating a Fragment Database

C. The cnx.bat File

The cnx.bat file

D. Searching for Fragments

   Searching for fragments
      Fragment database
      Fragment selection criteria
      Running a search
   Search Fragment Database palette
      List Proteins
      Pick Alpha Carbon Range
      Pick Alpha Carbon
      Undo Last
      Undo All
      Search Database
      With Bumps
      Display All Fragments
      Display Next
      Display Previous
      Select Display...
      List Residues
      Accept Fragment
      Anneal Fragment
      Reject Fragment
      Options...
      Finish
   Example: Using fragment searching to complete a model of renin
      Before you begin

E. Using RTF and PSF Modes

   RTF and PSF files and modes
      RTF mode
   Setting up a protein in PSF mode
      Organizing and separating segments
      Adding polar hydrogens
      Using CHARMm functions in RTF mode
      Using the Protein Editor
      Calculating a CHARMm energy
      Saving changes
      Problems

F. X-Ray - X-BUILD Command Conversions

Map management
Specific command conversions

G. Extend

   Where to find the program
   Introduction
      -extend
      -group (space group)
      -symops (file) [$HYD_LIB/symlib.sym]
      -limits (xmin xmax ymin ymax zmin zmax)
      -radial (x y z r)
      -pdb (pdb-file)
      -msf (msf-file)
      -input
      -boundary (value [0.0])
      -oformat (filename)
      -cutoff (cutoff [0.5])
   Examples
   General comments on the program