SHARP/autoSHARP user documentationSHARP/autoSHARP user documentation Copyright © 2001-2003 the Buster Development Group. All rights reserved. 1. Getting started 2. SHARP 3. autoSHARP 4. Phase improvement 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_pc.mtz wARP_pc.mtz model_._wARP_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 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 Get optimised values of anomalous scattering Calculate E values Finding sites 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 We're using colour coding throughout these documents to draw attention to important points or to clarify things: Variable name File name Directory name Important Very important Program name BDG program name Last modification: 18.11.04 Penn State Milton S. Hershey Medical Center ©2004 This page was last updated on May 09, 2005 Contact Us