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KosinskiLab / AlphaPulldown

https://doi.org/10.1093/bioinformatics/btac749
GNU General Public License v3.0
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Generate Distogram and MSA coverage #256

Open Qrouger opened 4 months ago

Qrouger commented 4 months ago

Hi, I wanted to generate Distogram and MSA coverage plot for AlphaPulldown. As feature.pkl is not present, I had to modify the AlphaFold plot script to use the result_model[...].pkl from AlphaPulldown. If you want to generate these graphics, I shared the scripts on my github page just here: https://github.com/Qrouger/Utils_APD result_model_1_multimer_v3_pred_0 pkl dmap KikA_coverage_LDDT.pdf

Best regards. Quentin Rouger.

jkosinski commented 4 months ago

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

Qrouger commented 4 months ago

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.

gchojnowski commented 4 months ago

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

Qrouger commented 4 months ago

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

jkosinski commented 4 months ago

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?

gchojnowski commented 4 months ago

everything is there g

jkosinski commented 4 months ago

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.