Peter Rose

I'm not sure why this problem only shows up with mmtf files. As you say, objects referring to each other is a typical problem. I believe mmtf creates bonds by...

I think we need to look at the readObject/writeObject methods. The adding of bonds uses a strange design pattern where bonds add themselves to the structure. Perhaps we need to...

Jmol's mmtf example page (V 14.20.4) seems to work: https://chemapps.stolaf.edu/jmol/jsmol/mmtf.htm On Tue, Aug 8, 2017 at 3:30 AM, Aleix Lafita wrote: > Could that be a bug in jmol's decoder?...

Interesting case! How about checking if the centers of mass of the subunits are too close (based on a threshold) and if they are below a threshold, switch to the...

I support a long-term solution. All the workarounds cause problems as you’ve mentioned below. -Peter

In Jmol you can access a particular chain by chainId and symop, for example :A&symop=3. I think this would fit quite well with BioJava which operates on chains, rather than...

I'm not aware of any plans for multi-structure files. Since each data section starts with data_xxx, it should be straight forward to have multiple structures in a single file. You...

Thanks for looking into this. I'm using Jupyter Lab version 1.2.6. I'm trying to visualize a knowledge graph I've created in this repo: https://github.com/sbl-sdsc/coronavirus-knowledge-graph There is a Launch Binder link,...

@merqurio we are trying to use neo4jupyter for our coronavirus KG. If you have a chance, could you look into the 0.2.0 milestones? You could save a life!

@DoubleBite yes, jupyter notebook works, but we have switched all our work to jupyter lab. On Thu, Jun 11, 2020 at 12:04 AM DoubleBite wrote: > @pwrose > > Using...