IHM Meeting Summary Jun 23 2017

IHM Meeting Summary Jun 23, 2017

Attended by Ben Webb, Tom Goddard, Mike Goodstadt and Brinda Vallat

1. Issue 37: Tom will generate the transformed dcd files and then Ben will update the mmCIF files accordingly.
2. Issue 9: Tom will work on visualizing the multi-state exosome complex on ChimeraX.
3. Issue 38: This seems like the right approach to define chemical moieties involved in crosslinks. However, more precise definitions may be required to capture the details of the reactive atoms involved in crosslinks.
4. New issue to be created for generating permanent accession codes for entries in PDB-Dev (done) - Issue 39
5. Structures published in the following paper may be deposited in PDB-Dev: Zhu, J., Luo, B. H., Barth, P., Schonbrun, J., Baker, D., and Springer, T. A. (2009). The structure of a receptor with two associating transmembrane domains on the cell surface: integrin αIIbβ3. Mol. Cell 34, 234-249. Since the structures are atomistic, MAXIT may be used to convert the coordinates in PDB format to mmCIF format. The tables specific to I/H methods (such as ihm_struct_assembly, ihm_model_representation, ihm_dataset_list, ihm_starting_model_details) may require additional scripts.
6. Modeling of the Spindle Pole Body using IMP: Manuscript submitted for publication; structure will soon be deposited to PDB-Dev. Modeling uses restraints derived from FRET, SAXS, EM, yeast two hybrid, crystal structures and homology models. New categories may be added to the dictionary in order to describe the restraints.
7. 3D structures of Genomes generated using information derived from Hi-C and 3C experiments: Mike gave an overview of the data involved and modeling carried out (top-down from Hi-C data and bottom-up using molecular dynamics) to generate the coarse-grained models. The data and models will be shared so that we can figure out the best way to convert these to mmCIF data files.
8. Next meeting will be on Thursday, June 29th, at 12:00 noon Eastern time.