Chris Brasnett

If/once you've merged the codecov update in #565 I'll merge main into here and I guess that'll fix the tests

A solution to make everyone happy, remove the NW alignment altogether and just check the seqres directly against the pdb entries. (thanks @Tsjerk for the discussion)

@pckroon Noticed one minor issue with how this was fixed. In the case where we have >1 chain in the protein, the mutation is looked for across all chains and...

Thanks, not sure I have time to address this week but I'll try to start next. It would be good to try and address #512 at the same time, but...

ha, understood! I'll address this soon then, and maybe we could work something out for the rebuilding issue in the new year?

sweet, I'll drop you a message then

I'm not certain, but I think adding again there would be degenerate anyway? VirtualSiteCreator gets called both in the Go model and if `args.water_bias` is used, so I think just...

This *should* bring things in line with polyply for generating topologies of idps. Maybe this is the right approach, maybe it isn't, but here's some kind of implementation either way....

From what you've described, it sounds like you're trying to generate Martini topologies for a whole system in one go. Have you tried generating a single topology of your protein...