Comments (3)
Also discussed here: sokrypton/ColabFold#76
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Hi Deniz,
Certainly it can be achieved in AlphaPulldown. You can use make your selected structures to replace the default template features when running run_multimer_jobs.py
by adding the flags --multimeric_template --description_file=/path/to/descrption.csv
multimeric_template
is a boolean flag that will inform AlphaPulldown to look for customised template structures and replace the original template features. ``ยด description_file.csv```should be in the following format:
protein_A,xxx.pdb,C
indicating your query sequence protein_A
should be mapped to chain C your pdb file xxx.pdb
, suppose you already had protein_A.pkl
In addition, the actual sequence of the chain in the PDB does not necessary have to be the same as the protein_A sequence, as AlphaPUlldown will realign the sequences anyway but it will always better if your template covers as many residues as it can.
On the other hand, you can also regenerate the pickle files as described here: https://github.com/KosinskiLab/AlphaPulldown/blob/main/manuals/example_3.md
Yours
Dingquan
from alphapulldown.
Please also refer to the TrueMultimer sections of the new manual:
https://github.com/KosinskiLab/AlphaPulldown?tab=readme-ov-file#14-run-with-custom-templates-truemultimer
https://github.com/KosinskiLab/AlphaPulldown?tab=readme-ov-file#25-run-with-custom-templates-truemultimer
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Related Issues (20)
- Multiple feature directories HOT 2
- Improve resume predictions HOT 1
- GPU seems not working when run_multimer_jobs.py HOT 5
- Runtime of each prediction HOT 1
- Use DEFINE_list for model_names flag HOT 3
- Clean duplicating functions/ redundant code
- 'ranking_confidence' is not in the result.pkl file after the update HOT 10
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- rename_colab_search_a3m.py does something unintended HOT 4
- output jupyter notebook is empty HOT 2
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- create_notebook doesn't work on AlphaPulldown 2.0b? HOT 8
- Remove result pickles HOT 1
- question: correct pipeline for mmseqs alignments in alphapulldown?
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