How to turn off templates on AF3 server?

[HenriettaHolze]

Dear AF3 team,

I cannot manage to run template-free on the AF3 server. I've tried using "templates": [] and "useStructureTemplate": false in the json I upload. But in both cases the results contain templates in the templates/ folder and the results are identical to running with templates.

When I set the "maxTemplateDate": "2025-02-03" I am also not sure if this is respected. When I "clone and reuse" the job, this setting does not show up in the "Template settings" anymore. So I don't know if the server applies the parameter in the first place.

Many thanks for your help,
Henrietta

[Augustin-Zidek]

Hello, thanks for reporting this. We haven't been able to reproduce this. Could you get in touch with us via alphafold@google.com and provide the exact input JSON that you used?

[HenriettaHolze]

It seems like I cannot simultaneously supply unpairedMsa and set useStructureTemplate: false. Either parameter separately works. Maybe I missed that in the documentation.

[Augustin-Zidek]

When I set the "maxTemplateDate": "2025-02-03" I am also not sure if this is respected. When I "clone and reuse" the job, this setting does not show up in the "Template settings" anymore. So I don't know if the server applies the parameter in the first place.

Could you provide the JSON for this one (you don't have to include the protein sequence, it is not essential for reproducing this)? Did you use that in combination with useStructureTemplate: false?

[HenriettaHolze]

This should reproduce the behavior. I stripped the MSAs to a few sequences due to file size.

test_templatefree_reproduce.json

No, setting "useStructureTemplate": false and "maxTemplateDate": "2025-02-03" throws an error during file upload. But I think it is the same issue, that I am using maxTemplateDate in combination with unpairedMsa which does not work.

[Augustin-Zidek]

Thanks, we will reproduce and get back to you.

[Augustin-Zidek]

Bug confirmed and fixed on our side. I will let you know once it is rolled out.

[HenriettaHolze]

Wonderful, thanks! I appreciate the fast response.

[HenriettaHolze]

Hi, I see that you've updated the server. Could you confirm that previously the parameter maxTemplateDate was ignored if used in combination with unpairedMsa? Then I have to remove the parameter for future runs if I want them to be comparable with previous runs. Thanks.