Downloaded event maps misaligned? - investigate

[phraenquex]

For this CHIKV download:

In Fragalysis (NGL), the event maps aligns perfectly with the ligand; but when I download the maps and ligand and display them in pymol, they're offset. Bug in upload/download chain, or pymol weirdness?

[tdudgeon]

I believe there is an "offset" property that is defined in the maps that handles the periodic boundary problem. This is handled by NGL (see #1238). Presumably this is not handled in pymol and presumably the downloaded files display fine if opened in NGL?

[phraenquex]

Decision to take: do we care about pymol users.

(Conor says coot does use offsets correctly. We don't know about other things, e.g. ChimeraX.)

Minimal action: document correclty in the PDF. #1259.

[mwinokan]

From Daren:

Caught up with Conor and he pointed out NGL viewer uses origins in map file but Pymol and Coot don't which fits with what I've seen with Jasmin's data. So we believe the files being served up are indeed the same as those being displayed.

I think the vast majority of users will be using Pymol/Coot and Conor said it's feasible for him to create multiple map files as suggested (i'm guessing we just need 2) so can we go ahead and create a ticket for that?

Event maps in the NGL viewer and download are the same, but when viewed with PyMol/Coot they are offset as the origins are not used.

@ConorFWild please see #1448 for the changes needed to XCA