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kalininalab / alphafold_non_docker

AlphaFold2 non-docker setup
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The B-factor field (pLDDT confidence measure) of the output PDB file is always 0 #11

Closed Yuangaga closed 3 years ago

Yuangaga commented 3 years ago

Hi~Thanks for your work. And I have run alphafold without docker successfully following your tutorial. But the output PDB file may be something wrong:

The B-factor field, which is stored pLDDT confidence measure, of the output PDB file is always 0 in my test work based on the example query.fasta.

WechatIMG281

截屏2021-08-16 下午2 31 34

And I saw the same result in your dummy_test/query/anked_0.pdb. WechatIMG282

Then I tried to use the AlphaFold Colab notebook demo for validation. The result from AlphaFold Colab notebook seems no problem.

WechatIMG283

截屏2021-08-16 下午2 41 42

So is there any way to fix it ? Thanks a lot.

sanjaysrikakulam commented 3 years ago

Hi @Yuangaga

Sorry, our non-docker version is only a wrapper script to run AF2. Unlike the colab variant, we do not directly work with the AF2 codebase in the non-docker version. Maybe raise a ticket in the AF2 github repo and they can add the feature to their codebase.

sanjaysrikakulam commented 3 years ago

Hi @Yuangaga

Seems like AF2 has recently added this feature to add the B-factors to the PDB file. So, can you try it by pulling the latest version of AF2?

Yuangaga commented 3 years ago

Oh, I see it. Thank you very much. I will try it.

Yuangaga commented 3 years ago

Hi @Yuangaga

Seems like AF2 has recently added this feature to add the B-factors to the PDB file. So, can you try it by pulling the latest version of AF2?

Thanks! It worked.