dsehnal / binarycif Goto Github PK

Issue: Note the missing data on the right side of my box.

I can see how it might be intentional to always start the data set outside the box (nearer 0 0 0) and then stop before the final box boundary, but I suggest that if I say I want the surface within a certain box, then I want to see everything in the box, which means that allowing the data to extend just a bit further than the box in all directions if necessary is the appropriate thing to do.

Jmol can truncate as necessary to truly fill the box, but only if the data are returned.

The request is that the box be fully within the localized data returned, not just partly within it.

This was created in Jmol 14.28.2 using:

load *1eve
boundbox {e20:a}
isosurface BOUNDBOX EDS AS "box.eds"
isosurface "box.eds"

Hi there - just wanted to let you know, if you weren't already aware, that there is a basic BinaryCIF Python implementation in the python-ihm library, which supports the production of files (primarily in mmCIF format) for deposition in the PDB-Dev database. These are all integrative or 'hybrid' models, in that they are models fit to multiple experimental datasets, and are often coarse-grained. We've been experimenting with more compact representations of these models, and BinaryCIF seems promising so far.