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Does the template searching result contain query sequence's structure or not? #354

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psp3dcg opened this issue Jul 24, 2023 · 3 comments
Open

Does the template searching result contain query sequence's structure or not? #354

psp3dcg opened this issue Jul 24, 2023 · 3 comments

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@psp3dcg
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psp3dcg commented Jul 24, 2023

Context

If the template database (such as pdb100) contains the structure of the query sequence, will "hhsearch" return the structure information of the query sequence as a part of template? If so, how to remove the structural information of the query sequence itself from the template? Thank U~

Your Environment

Include as many relevant details about the environment you experienced the issue in.

  • Version/Git commit used: hhsuite 3.2.0
  • Server specifications (especially CPU support for AVX2/SSE and amount of system memory): Inter i7 10700, 64GB memory
  • Operating system and version: Ubuntu 18.04
@psp3dcg
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psp3dcg commented Jul 24, 2023

I usually use MSA generated by hhblits as input for hhsearch.

@milot-mirdita
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We add secondary structure information to the PDB70. You can disable secondary structure information by passing -ssm 0 to HHblits/HHsearch.

@milot-mirdita
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The PDB100 I created for ColabFold does not contain secondary structure information.

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@milot-mirdita @psp3dcg