Tom Goddard
Tom Goddard
In the current PyPi html2text converting a single backslash in html produces a single backslash in plain text. That seems right. But converting two backslashes in html produces 3 backslashes...
Current PDBDev entries such as 0001 have auxiliary files referenced by a DOI (eg. 10.5281/zenodo.1218053) in this case hosted by Zenodo. The speed downloading that data is abysmal. Currently trying...
It would be useful for visualization to have tables for user-deposited standard colors per asym_id, and a list of standard viewing orientations. I would read and use this information in...
The PDBDev validation should check that the external files referenced in the .cif exist. This does not appear to be happening now since PDBDEV_00000001.cif had bad references as reported in...
The IHM file format should use a different suffix than ".cif", I suggest ".ihm". This will allow software that reads this format to easily identify the dictionary in use, distinguishing...
Currently IHM starting model coordinates are in the ihm_starting_model_coord table. This is a redundant representation of atomic model coordinates usually represented by the mmCIF atom_site table. Important information such as...
It would be useful to describe the model representation used by IHM in a precise way but in higher level terms than the current IHM documentation https://github.com/salilab/mmcif/blob/master/dictionary_documentation/documentation.md Such a description...
The nup84, mediator and exosome examples are all based on published analysis done with IMP. To see if the format will accommodate hybrid models computed with other software we should...
The fly genome example final_2L_60_161.ihm has spheres 1-102 in two domains 1-50 and 51-102. While those two domains can be named using the ihm_struct_assembly table. John Westbrook notes that this...
Currently IHM inserts a new field ihm_model_id into the atom_site table. This complicates code that reads these files because it will likely use an existing mmCIF reader for atom_site that...