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When running the pipeline for other molecules I have issues when scoring the docked molecules and get errors like: 63%|██████▎ | 627/999 [27:50
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Hi!
Currently we have the functionality to handle pdb files with multiple models in it. It renders a trajectory control panel to navigate between models.
I am looking for a way to achieve th…
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@wxy-nlp I can not find pdb file [os.path.join('data-bin/scaffolding-pdbs/' + pdb + '_motif.pdb') ] when run scaffold_generate.py, Can you provide it?(https://github.com/microsoft/evodiff/tree/ma…
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Add a utility function to download PDB files from relevant repositories, with support for error handling and retry mechanisms.
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While performing motif scaffolding with RFdifussion, I have noticed that **the fixed segments in the generated PDB files do not exactly match those in the reference PDB file**. For example, I'm using …
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Hi,
In AlphaFold you have a the possibility to provide a template (or decoy) protein structure, this way skipping the MSA search, leading to faster predictions. Is this with Uni-Fold also possible…
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Currently the pLDDT masking fails if using PDB with multiple chains as pLDDTs are not extracted per chain.
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i cannot find these three files in the zip files PythonConsoleControl.pdb,NpsRuntime.pdb,NavisPythonShell.pdb. i have copies the files from Noexclude.txt and exclude.txt files into the two directories…
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In trying to run the EVcouplings pipeline, I couldn't download the MMTF files needed. Then I found the following message from RCSB:
"As of July 2, 2024, RCSB PDB will no longer serve PDB data in th…
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I'm not sure where the best place to put this is between gtirb-pprinter, gtirb-rewriting and here, so please let me know and I can reopen this in the best repo.
While developing instrumentation usi…