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NaN values in the output coordinates #243
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Oh thank you for reporting this. We had a big change yesterday on the colabfold system to improve the compile behaviour of AlphaFold2. Could you please try to run your example using an old version of the notebook: https://colab.research.google.com/github/sokrypton/ColabFold/blob/v1.3.0/AlphaFold2.ipynb |
Hi @martin-steinegger , no problem! My input sequence is: PRDGYKFSLSDTVNKSDLNEDGTININGKGNYSAVMGDELIVKVRNLNTNNVQEYVIPVDKK I am currently modeling the sequence through the older version of the notebook. One important thing that I forgot to mention: This problem that I had only happens when I try using custom templates. If I try to predict the homooligomers without any custom templates it does work properly. |
That's good news in some way. Thank you so much. |
No problem! But I am not really sure if the template itself is the problem. In v1.3.0 although I selected use_templates there isn't the option to select a custom one, so the pipeline found the structure 3zjx by itself, which is the same sequence but a different conformation of the 6rb9 that I used as a custom template in the latest version. I'm sending the mmCIF file that I used, I just added .txt to the extension so that github would allow me to upload it |
Thank you so much. I tried to run your sequence with your custom template but it did not crash. |
Interesting... I used 6rb9.cif, I only added this .txt extension so I could upload it here |
Oh, just to clarify, I can actually predict the monomer using templates with the sequence I posted above, what I can't do is predict the oligomers: |
Oh this indeed causes the same issue. It is quite odd. if I run it with a cpu I do get a result but a pretty bad one.
Somehow the template information is harmful. The aligned coordinates seem to be quite fragmented too. |
In Google Colab I couldn't make it work running solely on cpu as well, but something really interesting happened now. I was trying to run this sequence with the template either on Google Colab or on the local installation I had on our cluster, and both failed. But now I've managed to run it locally on my workstation with the template: $ colabfold_batch . results_test_templates_yes_path --templates --num-models 1 --num-recycle 1 --custom-template-path . 2022-06-16 13:18:03,746 Running colabfold 1.3.0 (1c9b056) If you require more MSAs, please host your own API and pass it to I really don't know how this is happening... maybe there are some differences in the installation |
I have the same issue as f-meireles reported (NaN coordinates with homooligomer mode) with completely different input sequences. I used the batch notebook. |
@martin-steinegger @ykagaya noted the JAX version in |
Yes, it seem to be a jax related issue. We will downgrade it again soon. |
jax 0.3.7 works something broke in jax 0.3.8... |
@YoshitakaMo found the source of the bug. We submitted a bug report! |
We fixed it in colabfold. Please give it a try. |
Hi! I upgraded my colabfold installation but unfortunately now there seems to be another type of error: $ colabfold_batch . results_rec1_yestemplates_afterfix --model-type AlphaFold2-multimer-v2 --num-recycle 1 --num-models 1 --custom-template-path . --templates 2022-06-17 09:50:37,663 Running colabfold 1.3.0 (4f88237) If you require more MSAs, please host your own API and pass it to And when I try to run it without any templates I am getting this: Traceback (most recent call last): But since I am getting an error without using templates as well this might mean that I have messed up during the upgrade, I will try purging my current installation and re-installing colabfold. EDIT: I still can't get it to work, even after re-installing it from scratch. |
Did you try the notebook? Yeah maybe wiping everything locally might help. |
I just tried it and it and the notebook does work. I will try to see what is wrong in my local installation EDIT: Alright, now it's working! I can run complexes locally with custom templates. This last time I was actually having some trouble with my local installation. Thank you all very much for your help, @martin-steinegger @sokrypton! |
Yay! Thanks for reporting the issue! |
Expected Behavior
Greetings everyone,
I am trying to use a custom template to guide the building of a homooligomeric model.
Current Behavior
But for some reason the models that are "built" are lacking all of the coordinates, presenting only NaN values. This happened to me both in my local colabfold installation and in the colabfold notebook:
This problem only happens when I try to run homooligomers. If I try to predict a single chain of the same input sequence the software works properly:
I tested it with several fragments of the sequence that I am using and several numbers of chains (3,5,6,8).
Thank you in advance for your attention and please let me know if I can provide more useful info.
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