Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Is the use of template a must for running FastFold? #111

Open
kwanUm opened this issue Nov 21, 2022 · 1 comment
Open

Is the use of template a must for running FastFold? #111

kwanUm opened this issue Nov 21, 2022 · 1 comment
Labels
question Further information is requested

Comments

@kwanUm
Copy link

kwanUm commented Nov 21, 2022

Hi, I'd like to run FastFold for a long sequence with no templates. Is this setting supported by FastFold?

I'm building an MSA only from Uniref90 DB for starters.
@Shenggan Shenggan added the question Further information is requested label Nov 23, 2022
@Shenggan
Copy link
Contributor

Similar to AlphaFold/OpenFold, you can set flag c.model.template.enabled = False in fastfold/config.py to disable template.

And you can refer to

FastFold/fastfold/model/hub/alphafold.py

Lines 255 to 256 in 8a59989

# Embed the templates + merge with MSA/pair embeddings
if self.config.template.enabled:

to see the part that this flag affects.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
question Further information is requested
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@kwanUm @Shenggan