1. Getting started

• What SHARP can do
• Short introduction to autoSHARP
• SHARP/autoSHARP tutorials

2. SHARP

• Chapter 0: Description of the SHARP manual
  • Intended audience
  • What this document is about
  • A quick outline
  • How to use this Manual
  • Authors

• Chapter 2: What SHARP can do
  • Phasing scenarios
    • Introduction
    • SAD
    • SIR(AS)
    • MAD
    • MIRAS
    • MAD + native
    • Others
  • Residual maps
  • Density modification
  • External phase information

• Chapter 3: The environment of SHARP
  • The CCP4 suite of programs and the MTZ format
    • Introduction
    • MTZ :a format for crystallographic data
    • How to prepare MTZ files for SHARP
  • The SHARP Control Panel
    • Introduction
    • Help
    • Documentation
    • Tutorials
    • Change password
    • Preferences
    • Start
    • Request
    • Examine
    • Delete
    • Browse
    • About
    • Mail
  • The Preferences page
    • User level
    • Job submission scheme
    • General layout of maps
    • Display
    • Display viewer
    • Peak picking
    • Skeletonization
    • Objects
    • Results options
    • Output options

• Chapter 4: How to tell SHARP what to do
  • General information
  • Preparing input for refinement jobs
  • Field-by-field description of the input pages
    • Identification
      • Project name
      • Title
    • Calculation Options
      • Outlier rejection using likelihood histogram
      • ML parameter refinement
      • Residual (Log-Likelihood Gradient = LLG) maps
      • Centroid electron density map
    • Datafile, Symmetry and Cell
      • Datafile
      • Spacegroup
      • Cell
    • Other information
      • Chemical composition of the asymmetric unit
      • External phase information
  • Geometric Site Editor
    • Adding one or more G-sites
    • Inverting hand
    • Setting refinement flags
    • Deleting G-Sites
  • What is a reference dataset ?
    • Definition
    • How to choose the correct reference ?
  • C-Site Editor (Compound level)
    • Adding or deleting a C-site
    • Specifying a C-site
  • T-Site Editor (Crystal level)
    • What are "tunable"sites p?
    • Specifying a T-site
    • Refining temperature factors
    • Setting refinement flags
  • Wavelength level editor
  • Batch level editor
    • Column assignment
    • Scaling parameters
      • Estimation of reference scaling parameters: pseudo-absolute scale
      • Estimation of non-reference scaling parameters: relative scale
    • Global non-isomorphism parameter
    • Model imperfection parameters
    • Anomalous scattering properties by atom type
  • Checking the calculation

• Chapter 5: What SHARP is telling you
  • Introduction
    • Preparation of data
    • ML Refinement
    • Residual maps
    • Electron-density maps
  • Reading the input parameter file
    • Cell information
    • Symmetry information
    • Atomic scattering information
  • Preparation of data
    • Changing the resolution bins
    • Accepted reflexions
    • Initial outlier rejection
    • Computing statistics
    • Estimation of the absolute scale
    • Estimation of the relative scale
    • Estimation of lack of isomorphism
  • Maximum-Likelihood refinement
    • Outlier rejection using likelihood histograms
    • List of refined parameters
    • Refinement step in parameter space
    • Step length
    • Lack of isomorphism
    • Other statistics
  • Residual maps
    • Type of residual map
    • What to look for in a residual map
  • Electron-density map
    • Statistics
    • Displaying an electron-density map
    • Solvent flattening (density modification)

• Chapter 6: When trouble strikes
  • Browser
  • Permissions
  • Step-by-step

• Appendix 1: What can I do with results from SHARP?
  • resid.mtz
  • eden.mtz
  • eden-unique.mtz
  • eden_flat_<solvent fraction>pc.mtz
  • wARP_<solvent fraction>pc.mtz
  • model_<project>.<id>_wARP_<solvent content>pc.pdb

• Appendix 2: How to use SHARP under UNIX
  • Introduction
  • Running SHARP
  • Running autoSHARP
  • Running solvent flattening
  • Running automatic building

• Appendix 3: Detailed description of the Sharp INput file
  • Introduction
  • General keywords
  • G-Sites
  • Compound
  • Crystal
  • Wavelength
  • Batch

3. autoSHARP

• Chapter 1: Short introduction to autoSHARP
  • What you need
  • Files
  • Outline

• Chapter 2: Telling autoSHARP what to do
  • Main autoSHARP Control Panel
    • Preparation
    • Project identifier
    • Title
    • Molecular weight, number of residues, sequence
    • Spacegroup
    • Heavy atom types, known positions
    • What to do?
    • Resolution limits
    • Dataset identifier
    • Wavelength, f', f''
    • Datafile
    • Column labels
    • Cell parameters
  • Advanced settings

• Chapter 3: Interpreting the autoSHARP output
  • Checking supplied information
  • Converting files
  • Extracting additional information
  • Collecting and analysing all data
  • Adding test set column
  • Scaling/analysis of merged data
  • Additional analysis (NCS, sequence ...)
  • Get optimized values of anomalous scattering (RANTAN only)
  • Calculate E values (RANTAN only)
  • Finding sites with RANTAN
  • Finding sites with SHELXC/SHELXD
  • Create a SIN file
  • Run first round of SHARP
  • Automatic interpretation of residual maps
  • Run final round of SHARP
  • Running density modification
  • Running automatic building

4. Phase improvement and interpretation

• Chapter 1: Basics
  • Introduction
  • Real space
  • Restraints and constraints
  • Solvent content
  • Quality of initial phases
  • Non-crystallographic symmetry (NCS)
  • Solvent envelope
  • Methods
    • Solvent flattening
    • Solvent Flipping
    • Histogram matching
    • NCS averaging
    • Skeletonization
    • Sayre's equation
  • Cyclic method

• Chapter 2: Phase Improvement and Interpretation
  • Introduction
  • Density modification
    • Solvent fraction
    • Resolution range
    • Real solvent content
    • Starting solvent content
    • Radius of solvent sphere
    • Flipping factor
    • Mean density
    • min / max density truncation in "protein" region
    • starting DM run ?
    • Including available partial model
  • NCS detection
    • Molecular weight of monomer
    • Number of rotations & translations to test
    • Monomer positions
    • Ignoring crystal symmetry
  • Automatic building using ARP/wARP
    • Number of residues
    • Total number of cycles
    • Number of cycles between rebuilding
    • Sequence file
  • Utilities
    • Optimal solvent content
    • External phases
    • Difference Fourier

Notation

• Variable name
• File name
• Directory name
• Important
• Very important
• Program name
• BDG program name