Welcome to sfftk’s documentation!

Note

Looking for a graphical aid to using sfftk? Try out the online version: the Segmentation Annotation Tool.

Note

Only interested in working directly with EMDB-SFF files? Checkout the minimal sfftkrw package.

Note

Visualise EMDB-SFF in UCSF ChimeraX

EMDB-SFF files (.hff and .sff) can now be visualised in UCSF ChimeraX thanks to the wonderful efforts of the UCSF ChimeraX team! Get the daily build here. Convert .json EMDB-SFF files to .hff or .sff using:

sff convert file.sff -f json

Contents

• EMDB-SFF Toolkit (sfftk)
  • Introduction
  • Getting Started
  • Features
• Converting Files To EMDB-SFF
  • Introduction
  • Input Formats
  • Output Formats
  • Verbose Operation
  • Including All Segments
  • Specify Details
  • Changing The Primary Descriptor
  • Working with Multifile Segmentations
  • Converting Subtomogram Averages
  • Specifying Configurations To Use
• Annotating EMDB-SFF Segmentations
  • Introduction
  • Finding Notes
  • Viewing Notes
  • Modifying Notes
  • Configuration Settings
• Miscellaneous Operations Using sfftk
  • Viewing sfftk Version
  • Viewing File Metadata
  • Prepping Segmentation Files
  • Setting Configurations
  • Running Unit Tests
• Developing with sfftk
  • Introduction
  • Annotating EMDB-SFF Objects
  • Reading Application-Specific Segmentation Files
• Extending sfftk
  • Adding A Segmentation File Format
  • Adding A Search Resource
• sfftk packages
  • sfftk.sff module
  • sfftk.formats package
  • sfftk.readers package
  • sfftk.notes package
  • sfftk.core package

Indices and tables

• Index

• Module Index

• Search Page