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Preparing my pdb100 database #431

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kyle-davis279 opened this issue Feb 24, 2025 · 0 comments
Open

Preparing my pdb100 database #431

kyle-davis279 opened this issue Feb 24, 2025 · 0 comments

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@kyle-davis279
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I just downloaded the pdb100.tar.gz from the page that contains the foldseek databases (https://foldseek.steineggerlab.workers.dev/).

  1. It would be useful if you can provide a textfile that contains a list of the pdbid_chainid of all the entries in the pdb100 as I can easily use this information to download the mmcif files (which I need in another analysis).
  2. If I want to prepare my pdb100 database of a particular local pdb folder, do I have to do a two-step clustering? Meaning I first cluster using --min-seq-id 1.0 option and then compile all the representative structures from the previous step and run another clustering using -c 0.95 option?
  3. Does using --min-seq-id 1.0 and -c 0.95 options in a single command produce the same output in No.2?
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