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PDBFixer not working some PDB file #227
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Without providing the PDB file that causes the problem there's really no way to diagnose. If there's a PDB from RCSB that fails to parse, you can just provide the code. Otherwise, can you attach it here so we can try to reproduce the problem? |
Thank you so much for replying.I added this unreaded file in the following: |
Your file begins with several lines that aren't part of the PDB format.
You need to remove those lines, or else prefix each one with "REMARK" to indicate that it's a comment. |
for me fixer.addMissingAtoms() it is not working and showing KeyError: 'NDG' |
I found a solution for your problem:
Set the missingResidues as blank, and continue with removeHeterogens will work. |
Hi,
Before running Openmm, I would like to edit some protein structure via PDBFixer. But while Fixer read some PDB, some are not read. What can I do in order to be read PDB structure? By the way PDB structure is a predicted model not cystral.
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