sokrypton / sokrypton/ColabFold
Tetramer running crashed and selenoprotein with amino acids selenocysteine (U) prediction issue
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Description
I have an issue in predicting the structure of a protein that contains a selenocysteine. The unrelaxed or relaxed pdb has a missing residue corresponding to the selenocysteine position and relaxation failed due to missing atoms. In this case, will it be accurate for predicting the structure by replacing the Selenocysteine by cysteine? Did aflphafold sequence input recognize the U amino acids as selenocysteine? I did not have error when I input the sequence with U.
Meanwhile, when I input tetramer protein sequence. It said "your session crashed after using all available RAM.” In this case, is it necessary to upgrade the Colab to pro+?
Thanks!
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First steps
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Research direction
No files, tests, or entry points are named. Review the ColabFold sequence-input and relaxation paths for selenocysteine, then investigate the tetramer run that exhausted Colab RAM; the report is complete only when both U handling and the memory failure have a documented resolution.
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Assessment
- Tech stack
- jupyter-notebook
- Domain
- bioinformatics, machine-learning
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100