Generate Distogram and MSA coverage about alphapulldown HOT 7 OPEN

Hi Quentin,

Thanks for letting us know! Would you like to integrate it with AlphaPulldown or rather keep it in a separate repository? If the former, we can consider that internally (we might have some code for this already in @gchojnowski analysis library, just not exposed in scripts). If the latter, we could provide a link to your lib in our readme files. Just let us know.

Best,
Jan

from alphapulldown.

Hi, thanks for your reply. If you were planning to make these plots in the future , I think it is not necessary for the code to be directly integrated into your pipeline. Otherwise I would like to integrate it.

Best,

Quentin Rouger.

from alphapulldown.

Hi Quentin,

we have a code generating flattened distograms in the suite already and just need to expose it. I'm wondering, do you plot average predicetd distances on the distance map?

g

from alphapulldown.

Hi @gchojnowski , Yes I think the predicted distance is an average. It generated from result_*.pkl ["distogram"]["bin_edges"] and ["distogram"]["logits"]. The distance is not made between Ca-CA or Cb-Cb.

Best,
Quentin Rouger

from alphapulldown.

Hi, thanks for your reply. If you were planning to make these plots in the future , I think it is not necessary for the code to be directly integrated into your pipeline. Otherwise I would like to integrate it.

Best,

Quentin Rouger.

OKay, and @gchojnowski, we also have have functions for MSA plotting in ColabFold style, right?

from alphapulldown.

everything is there
g

from alphapulldown.

OK! I think we should expose them in scripts as well. I will create a separate feature request for that.

In any case, @DimaMolod @dingquanyu What do you think about adding a short one-sentence comment and link to https://github.com/Qrouger/Utils_APD in the analysis section of our manuals? Or in some separate section called "Integration with other tools".

One potentially useful unique feature @Qrouger has is the export of restraints for Rosetta based on the distogram.

from alphapulldown.