Bsoft 1.5.0
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Bsoft 1.5.0
User's Manual
Bernard
Heymann
Table of Contents
1. Introduction
Background and history
Features
2. Installation
Requirements
Graphical Interface: Tcl/Tk
Unpacking and compiling
Unix
Mac OSX
VMS
Windows/Cygwin
32 bit versus 64 bit versions
Environment
Unix
Mac OSX
VMS
Windows/Cygwin
Associated packages
PFT2/EM3DR2
Radon
3. Getting started
The Command Line Interface
Bsoft program types
Image processing programs
Molecular processing programs
Micrograph parameter processing programs
Low level file manipulation
Graphical interface
Image manipulations
4. Geometry and Conventions
Coordinate system
Discretization/digitization/sampling of space
Rotations and views
Origin: Placement of objects
Point group symmetry
Helical symmetry
Crystallographic symmetry
5. The Image Data Model
The image as a five-dimensional data set
Data types
Image file formats
Raw files - custom interpretation of image files
6. The Molecule Data Model
The molecule group hierarchy
Sequences
Atomic and sequence file formats
7. The Parametric Data Base
The STAR format
Internal hierarchies of structures
The micrograph parameter hierarchy
STAR files for micrograph parameters
Parameter files for image and molecular processing
atom_prop.star
res_prop.star
symop.star
.krn files
8. The Representation of Models
Model parameters
Model file formats
Glossary
References
List of Tables
2.1.
Platforms on which Bsoft has been compiled and tested
4.1.
Point group symmetry conventions
5.1.
Bsoft image data types
5.2.
Image file format features (as implemented in Bsoft)
5.3.
Tag-value descriptions for custom interpretation of image files
6.1.
Atomic and sequence file formats
User's Manual