Aleix Lafita

Since the MMTF format is actually an efficient serialization of a `Structure`, I was thinking that we could replace the read and write object methods of the `Structure` class with...

What is exactly the idea you have in mind? I propose two methods for coloring the subunits: 1. Get a List of ResidueRanges for each protodomain (symmetric subunit), so that...

I created a new issue for StructureAlignment visualization #396, so that we have two threads about molecular visualization: one for symmetry (which should include internal and quaternary symmetry) and one...

I assign this issue to the 5.0 milestone because it is a major API change that will not happen before 4.2 release.

I have a use case for a parser of sequence alignment files, and since **BioJava** can transform them to `Strings` in some formats, it is a disadvantage not being able...

>Could that be a bug in jmol's decoder? Yes, it is a problem in Jmol decoder, because opening an MMTF file in a simple JmolPanel shows the same error. >The...

We are using version 14.6.2 in BioJava, but strangely when I download the desktop version (same as the one in BioJava) showing an MMTF structure works, but when I try...

I updated to Jmol 14.29.17 and the error is still there. I will submit a PR reverting to using mmCIF until we figure out what is the problem. For the...

I did a bit of research and the problem has to be when converting the MMTF object into an OutputStream. https://github.com/biojava/biojava/blob/359dce819e7678879ae41301b11fa268f92e81d1/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.java#L130-L153 A possible test could be to save the OutputStream...

Hi @sanshu, sorry for the delayed reply. Do you think you could submit a bugfix pull request for this?