Aleix Lafita

Adapting a **global** alignment into a **semiglobal** alignment is very easy. For the alignment of two sequences of length n and m, the steps are: - Initialize the first row...

As in #629, reverting #570 fixes this issue. There seems to be problems when passing the MMTF structure to Jmol and some information is missed, causing a version of the...

These assemblies have very elongated subunits and large interfaces, so this might be another property to identify them and switch to the all-atom comparison.

Hi @r614, we do not allow directly pushing changes to the main repository. You should instead fork the biojava repository to your account, push the changes there, and then open...

I would also like to give my opinion on the topic, because I encountered some problems while doing **structural alignments with Biological Assemblies (BA)**. The structural alignment algorithms were designed...

There seems to be different opinions about how the **biojava-tools** can be organized and different implementation and library preferences. I guess we all agree that it would be beneficial to...

In my opinion it is only important to take into account the contacts in the **biological assembly**. Secondary Structure (SS) formed at the crystal contacts is artificial, and probably without...

Some of the things that could be improved in SS assignment were discussed in #112. We decided to stick with the **DSSP** conventions, since it has been the standard. However,...

Ok, let's create the test and see what is missing then.

Check issue #18