Re: [PyMOL] Deprecation of MMTF-format files for the PDB archive

[Robert H. <ha...@st...>]

Jose, I have a few questions about the BCIF format. Adding pymol-users
because there might be interest there as well (at least among developers).

First, at PDBe, where is the link for downloading BCIF files for a given
structure?

I only see this, for example, at  https://www.ebi.ac.uk/pdbe/entry/pdb/4hhb
[image: image.png]
Any plan to include BCIF there?

Second, I am not finding a definitive description of distinguishing among
MMFF and various types of BCIF files, since the same internal MessagePack
format is used for all.

Is there a reliable and future-proof way of doing this short of parsing the
whole byte stream with a MessagePack reader and checking for map keys or
values? That does not seem to me a very efficient way of processing byte
streams.

I had thought perhaps the initial map value for "encoder" would suffice,
but now I see that that is not reliable. For example, the density server
declaration in older BCIF files now refers to "volume-server".

Suggestions?

Bob