Front Matter
Introduction To The AFITT SUITE
Welcome To The AFITT Suite of Tools
Installation and Platform Notes
Licenses
Installation
Removal
Introduction To The AFITT GUI
Welcome To The AFITT Graphical User Interface
Differences From Previous Versions
Getting Started
AFITT Workflows
AFITT Supported Workflows
MMFF Settings
Hiding/Restoring Tips
How to Use AFITT
3D Scene
Wizard Operations
Basic Ligand Fitting
Refinement Dictionaries
Refmac Workflows
PHENIX Workflows
Buster Workflows
CNS/X-Plor Workflows
Ligand Builder
Choosing Data: Molecule/Maps Page
Selecting Ligands Or Proteins
Loading Maps
Looking Up Residues
Editing a Ligand
Protein Preparation
Applying New Residue Geometries
Inspecting Modified Residues
Find Density: Blobs Page
Selecting Analyzed Density
Advanced Modes of Operation
Fit Ligand: Fit Page
Looking at Results
Changing Ligand Residue Information
Selecting Ligands For Refinement
Covalent Bonds
Editing Ligands
Refine Complex: Refine Page
Refinement Dictionary
Refinement Parameters
REFMAC5 Script
PHENIX Script
Running REFMAC5
Running PHENIX
Notes about the Refinement Dictionary
Verify Refinement: Verify Page
Selecting a Residue
Ramachandran Plot
Finishing
Save CNS/X-plor
Save BUSTER
Save Fit - No Refinement Workflow
Molecule Manipulation
Editing 2D Molecules
Editing 3D Molecules
AFITT Usage
Command Line Interface
Release Notes
AFITT 2.4.1
AFITT v2.4.0
AFITT v2.3.0
AFITT v2.2.0
AFITT v2.0.1 (
August 2010
)
AFITT v2.0.0 (
February 2010
)
Citation
Theory
Fragment Fitting
FLYNN Usage
Overview
Minimum Requirements
Types of input ligands
Stereochemistry Enumeration
Refinement Dictionaries
Note about REFMAC5 refinement dictionaries
Note on the MMFF94 versus MMFF94s forcefields
Note on FLYNN and writing CIF Files
Command Line Interface
MTZ File Parameters
Advanced Parameters
Fragment Fitting Parameters
3D Construction Parameters and Torsion Driving Parameters
Example Commands
Results on The Gold Test Set
WRITEDICT Usage
Command Line Interface
Example Commands
ALIGNGRID Usage
Command Line Interface
MTZ File Parameters
Example Commands
ROTFIT Usage
Command Line Interface
Advanced Parameters
MTZ File Parameters
RSCC Usage
Advanced Parameters
Integration with Coot
Using FLYNN
FLYNN Advanced Options
Using WriteDict
Using the ROTFIT Interface
ROTFIT options
Installing Coot Interface
Release Notes
AFITT-CL 2.4.1
AFITT-CL 2.4.0
AFITT-CL 2.3.0
AFITT-CL 2.2.0
AFITT-CL 2.1.1
AFITT-CL 2.1.0
AFITT-CL 2.0.1
FLYNN 2.0.0
Citation
Bibliography
AFITT-2.4.1.2
Docs
»
AFITT Suite
AFITT Suite
¶
Front Matter
Introduction To The AFITT SUITE
Welcome To The AFITT Suite of Tools
GUI
Command Line
Highlights
Installation and Platform Notes
Licenses
Installation
Linux
Windows
Mac OS X
Removal
Linux
Windows
Mac OS X
AFITT GUI
¶
Introduction To The AFITT GUI
Welcome To The AFITT Graphical User Interface
Differences From Previous Versions
Differences from AFITT 2.3
Differences from AFITT 2.2
Differences from AFITT 2.0
Differences from AFITT 1.3
Getting Started
AFITT Workflows
AFITT Supported Workflows
MMFF Settings
Hiding/Restoring Tips
How to Use AFITT
3D Scene
Common Operations
Selection
Wizard Operations
Basic Ligand Fitting
Refinement Dictionaries
Fully Compliant Refinement Dictionaries
Covalent Bonds
Refmac Workflows
PHENIX Workflows
Buster Workflows
CNS/X-Plor Workflows
Ligand Builder
Choosing Data: Molecule/Maps Page
Selecting Ligands Or Proteins
Loading Maps
MTZ Maps
Looking Up Residues
Editing a Ligand
Protein Preparation
Applying New Residue Geometries
Inspecting Modified Residues
Find Density: Blobs Page
Selecting Analyzed Density
Pruning Blobs Using Distance to Protein
Advanced Modes of Operation
Locating Density at a Given Contour
Merging Density
Picking Density
Carving Density
Making a box that holds density
Fit Ligand: Fit Page
Looking at Results
Changing Ligand Residue Information
Selecting Ligands For Refinement
Covalent Bonds
Editing Ligands
Refine Complex: Refine Page
Refinement Dictionary
Refinement Parameters
REFMAC5 Script
PHENIX Script
Running REFMAC5
Running PHENIX
Notes about the Refinement Dictionary
Verify Refinement: Verify Page
Selecting a Residue
Ramachandran Plot
Finishing
Save CNS/X-plor
Save BUSTER
Save Fit - No Refinement Workflow
Molecule Manipulation
Editing 2D Molecules
Editing 3D Molecules
Advanced Molecule Operations
Independent Rotation/Translation of Molecules
Minimization
Monitors
Monitors
AFITT Usage
Command Line Interface
Release Notes
AFITT 2.4.1
Platform Support
Coot Support
Bug Fixes
AFITT v2.4.0
Major Features
Minor Features
Bug Fixes
Other
AFITT v2.3.0
Other
Major Features
Bug Fixes
AFITT v2.2.0
Major Features
Minor Features
AFITT v2.0.1 (
August 2010
)
AFITT v2.0.0 (
February 2010
)
Citation
AFITT COMMAND LINE
¶
Theory
Fragment Fitting
FLYNN Usage
Overview
Minimum Requirements
Types of input ligands
Stereochemistry Enumeration
Refinement Dictionaries
Note about REFMAC5 refinement dictionaries
Looking up known residues
Note on the MMFF94 versus MMFF94s forcefields
Note on FLYNN and writing CIF Files
Command Line Interface
Required Parameters
Optional Parameters
MTZ File Parameters
Advanced Parameters
Fragment Fitting Parameters
3D Construction Parameters and Torsion Driving Parameters
Example Commands
Basic Usage
Generating Reports
Choosing box regions of density
Choosing density close to residues
Choosing MTZ columns
Fragment usage
Results on The Gold Test Set
WRITEDICT Usage
Command Line Interface
Required Parameters
Example Commands
ALIGNGRID Usage
Command Line Interface
Required Parameters
Advanced Options
MTZ File Parameters
Example Commands
ROTFIT Usage
Command Line Interface
Advanced Parameters
MTZ File Parameters
RSCC Usage
Advanced Parameters
Integration with Coot
Using FLYNN
FLYNN Advanced Options
Box option
Check option
MMFF94s option
Using WriteDict
WRITEDICT Advanced Options
planarAniline option
Using the ROTFIT Interface
ROTFIT options
Fixup Rotamer
Fixup Pep-flip
Fixup MMFF/Shape
Installing Coot Interface
Installing WinCoot Interface
Release Notes
AFITT-CL 2.4.1
Platform Support
Coot Support
Bug Fixes
AFITT-CL 2.4.0
Platform Support
FLYNN
WRITEDICT
ROTFIT
AFITT-CL 2.3.0
Other
WRITEDICT
FLYNN
COOT Integration
AFITT-CL 2.2.0
WRITEDICT
FLYNN
AFITT-CL 2.1.1
WRITEDICT
FLYNN
AFITT-CL 2.1.0
WRITEDICT
FLYNN
AFITT-CL 2.0.1
WRITEDICT
FLYNN
FLYNN 2.0.0
Citation
Bibliography