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Backbone only search returns no hit. #256
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Our check to rebuild the backbone with pulchra seems to be incomplete. If both N and C are present, it will not try to rebuild the backbone, resulting in broken 3Di-tokens. Otherwise make sure you pass all of N, C, C-alpha and C-beta. |
Hello, many thanks to your quick response. I follow what you have mentioned, by passing only the alpha-C in my backbone but still it hits no matching records. I have attached one sample PDB file to this message and I would appreciate it a lot if you could help me check it out! HEADER HYDROLASE 19-JUL-00 1FCV You may ignore the PDB name which comes from my favorite protein entry. This backbone is from a CATH dataset so it mostly favor a reasonable structure. |
It is my bad. It seems I am working under 3Di+AA mode which corrupts everything totally. I could try local alignment mode with structure only. Anyway your response is really appreciated and I will report the result after giving a try. |
You can try the 3Di only mode. Foldseek doesn't work as well with 3Di only though, normally you'd need to pass both C-alpha and AA letter. Additionally, I don't think the pulchra backbone reconstruction works if you don't tell it what AA letter it is. |
Hello, I am having a naive question for Foldseek search. It is noticed in the paper that only alpha carbon relations will be extracted and be used to predict 3Di tokens. In this way, I manually curate a backbone only dataset with only N, alpha-C, and C atoms and construct corresponding PDBs from this dataset and later on run Foldseek search.
However, the results always say no hits are found.
I am not sure what has actually happened. Any help from you will be highly appreciated.
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