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Issue with output-format pdb vs output-format mmcif #209

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ameya98 opened this issue Mar 17, 2025 · 1 comment · May be fixed by #210
Open

Issue with output-format pdb vs output-format mmcif #209

ameya98 opened this issue Mar 17, 2025 · 1 comment · May be fixed by #210

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@ameya98
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ameya98 commented Mar 17, 2025

Hi, thanks for the wonderful implementation and repo!

I was experimenting with Boltz1 on a kinase:

version: 1  # Optional, defaults to 1
sequences:
  - protein:
      id: ABL
      sequence: GAMDPSSPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVNAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQES

With --output_format mmcif, I get something very reasonable as visualized in PyMOL:

Image

but with --output_format pdb:

Image

Am I doing something wrong?

@ameya98
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ameya98 commented Mar 17, 2025

Ahh, turns out the issue is in this line which messes up the column offset: https://github.com/jwohlwend/boltz/blob/main/src/boltz/data/write/pdb.py#L37C1-L38C1

        chain_tag = chain["name"]

which should be:

        chain_tag = chain["name"][0]

I'll send in a PR to fix!

@ameya98 ameya98 linked a pull request Mar 17, 2025 that will close this issue
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