Matt Horton

Likewise, this would be very nice – I just came across this issue myself when trying to display multiple several (e.g. 5) isosurfaces at different isovalues, to approximate a kind...

It looks like an implementation of order independent transparency is [imminent](https://github.com/mrdoob/three.js/issues/9977) for three.js, would this likely be transferrable to 3Dmol.js given that both are WebGL projects, or would it likely...

For this specific case, the `merge_sites` docstring claims `mode=='delete'` exists, does this definitely not work? An omission if so.

Thanks @adam-kerrigan! @jmmshn, do you have any thoughts on this? I remember you having issues with masking in `VolumetricData`/`Chgcar`.

That would be nice. Can you point to the CIF specification? Last time I looked into it, it was unclear to me how CIF defined bonds that crossed periodic boundaries....

Thanks @arosen93, that info on the periodicity labels `_geom_bond_site_symmetry_1` etc. was exactly what I was missing. More info on that tag here: https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Igeom_bond_site_symmetry_.html

@alex-l-m do you have a sample CIF file with bonding information that we could incorporate into pymatgen as a test case?

Hi @Anny-tech, thanks for the report. To be able to reproduce, could you supply the input structure too? My suggestions are: 1. Try `st1_1.diff(st2_1)` first. This calls the `.diff()` method...

Ok, for this application maybe [`StructureMatcher`](https://pymatgen.org/pymatgen.analysis.structure_matcher.html?highlight=structurematcher#pymatgen.analysis.structure_matcher.StructureMatcher) maybe more appropriate. This can compare structures based on atomic co-ordinates and tell you if they are the same structure or not. The `StructureGraph.diff`...

I'm also fine with these changes, but interested: > Use chgsum.pl AECCAR0 AECCAR2.pl directly. Don't read in the AECCARs via Pymatgen. This would require chgsum.pl to be in the PATH...