Overview

The IHM dictionary provides the data representation required for archiving integrative/hybrid structural models in PDB-dev.

This dictionary is an extension of the PDBx/mmCIF dictionary and provides the additional defintions required to handle integrative / hybrid models.

The IHM dictionary provides a mechanism to capture the following information regarding integrative / hybrid models:

• Defintions of multi-scale, multi-state, and ordered ensembles

• Descriptions of the starting structural models of individual molecular components obtained from experimental and computational techniques such as

  • X-ray diffraction
  • NMR spectroscopy
  • Computational models

• Definitions of the spatial restraints derived from a variety of experimental data such as

  • 2D and 3D electron microscopy
  • Chemical crosslinking mass spectrometry
  • Small angle scattering
  • Generic distance restraints obtained from biophysical and proteomics methods

• Referencing associated data from external resources

• Definitions of the ambiguities/uncertainties associated with the experimental data and preliminary validation metrics.

• Description of the modeling workflow

The I/H methods dictionary currently has over 30 new data categories and 300 new data items.

For more details regarding the dictionary, see the extension dictionary documentation.

For tips on structuring integrative modeling studies to be amenable to deposition, see this page.

Browse the wiki page for information regarding weekly meetings and descriptions of integrative modeling examples.

Organization of the repository

README.md - this file

ihm-extension.dic - IHM dictionary extension

dictionary_documentation - directory with detailed documentation regarding the data categories defined in the IHM dictionary along with examples.

mmcif_ihm_v0.xxx.sdb - The serialized dictionary for use with the RCSB mmCIF dictionary suite. This tool can be used to check whether a data file is compliant with the latest dictionary.

examples - directory with examples of integrative models compliant with the IHM dictionary

deposition - directory tracks support for generating IHM dictionary compliant data files by modeling software such as IMP.

Discussion

• Discussion on the file formats is conducted via email - please subscribe to the mailing list.

• We also meet weekly via Skype to discuss issues. All are welcome to join some or all meetings.

• To get an email every time this GitHub repository is updated, please subscribe to the IHM-mmCIF-commits mailing list.

Deposition of models to PDB-dev

In order to deposit models to PDB-dev in a semi-automated fashion, integrative/hybrid modeling packages need to support the mmCIF file format and the IHM extension. See the deposition directory for the current status of software support.

Visualization of integrative models

There is currently basic support for visualization of IHM mmCIF models in daily builds of UCSF ChimeraX.