List of fixes for failing test cases

openmm / pdbfixer

PDBFixer fixes problems in PDB files

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List of fixes for failing test cases #199

Open zhang-ivy opened 4 years ago

zhang-ivy commented 4 years ago

Here are the issues/fixes we discussed: 1) Wrong stereochemistry and clashes

Fix: Add restraints
Check atom and bond stereochemistry is biologically correct
Also check for bad bond lengths/angles and atom clashes?

2) Truncate and cap terminal and internal loops

Fix: Allow user to specify options OR edit fixer.missingResidues dictionary 3) Missing SEQRES
Fix: Add warning when the PDB is missing SEQRES lines

TO DO: prepare list of test cases (PDB ids) @jchodera @peastman @rafwiewiora

peastman commented 4 years ago

Fix: Add warning when the PDB is missing SEQRES lines

Should it always warn about this, or only if there are gaps in the residue numbers? If all residues in each chain have sequential numbers we know there can't be any missing loops in the middle, though of course we can't rule out missing terminal residues.

rafwiewiora commented 4 years ago

Should it always warn about this, or only if there are gaps in the residue numbers? If all residues in each chain have sequential numbers we know there can't be any missing loops in the middle, though of course we can't rule out missing terminal residues.

But what if you've used some tool that resets the residue numbers to sequential? I'd say always warn, better safe than sorry.