The generated proteins from the motif scaffolding example are bad

[kgao86]

Hi,

Now I am trying the motif scaffolding example in the tutorial:

complexa design configs/search_motif_local_pipeline.yaml
++run_name=motif_test
++generation.task_name=1YCR_AA

But the generated proteins are very bad, most of them are even not well folded:

Could you help double check to see what is going on? Thanks.

[nvdreidenbach]

Hello Complexa can only do binder design, ligand binder design, and AME based enzyme design. The motif pipelines are not meant to be run with the published checkpoints. Get Outlook for iOS<https://aka.ms/o0ukef>

…

________________________________ From: kgao86 ***@***.***> Sent: Wednesday, 15 July 2026 07:14:17 To: NVIDIA-BioNeMo/Proteina-Complexa ***@***.***> Cc: Subscribed ***@***.***> Subject: [NVIDIA-BioNeMo/Proteina-Complexa] The generation proteins from motif scaffolding example is bad (Issue #56) [https://avatars.githubusercontent.com/u/209533763?s=20&v=4]kgao86 created an issue (NVIDIA-BioNeMo/Proteina-Complexa#56)<#56> Hi, Now I am trying the motif scaffolding example in the tutorial: complexa design configs/search_motif_local_pipeline.yaml ++run_name=motif_test ++generation.task_name=1YCR_AA But the generated proteins are very bad, most of them are even not well folded: Screenshot.2026-07-15.at.10.12.27.AM.png (view on web)<https://github.com/user-attachments/assets/8166300d-83a9-4f46-8315-75e01b41790b> Could you help double check to see what is going on? Thanks. — Reply to this email directly, view it on GitHub<#56?email_source=notifications&email_token=AXI5JYP5YO7YL4KIR46WC235E6GTTA5CNFSL4Z3JMQ5C6L3HNF2C22DVMIXUS43TOVSS6NBYHEZTGMBRGE4TJJTSMVQXG33OVJZXKYTTMNZGSYTFMSSWK5TFNZ2KYZTPN52GK4S7MNWGSY3L>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AXI5JYN4GDCLHRTZPRM6P6L5E6GTTAVCNFSNUABGKJSXA33TNF2G64TZHMYTCNZXGMZDINZUGM5US43TOVSTWNBYHEZTGMBRGE4TJILWAI>. Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS<https://github.com/notifications/mobile/ios/AXI5JYLKCBS6V6MS6OXHGWT5E6GTTA5CNFSL4Z3JMQ5C6L3HNF2C22DVMIXUS43TOVSS6NBYHEZTGMBRGE4TJJTSMVQXG33OVJZXKYTTMNZGSYTFMSSWK5TFNZ2KUZTPN52GK4S7NFXXG> and Android<https://github.com/notifications/mobile/android/AXI5JYO64ZCONNBK245DBZD5E6GTTA5CNFSL4Z3JMQ5C6L3HNF2C22DVMIXUS43TOVSS6NBYHEZTGMBRGE4TJJTSMVQXG33OVJZXKYTTMNZGSYTFMSSWK5TFNZ2K4ZTPN52GK4S7MFXGI4TPNFSA>. Download it today! You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[kgao86]

Thanks