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.
Organization of the repository
README.md - this file
ihm-extension.dic - IHM dictionary extension
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
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.
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.