James Krieger

PDBFixer cannot handle nucleic acids with residue name N

5

``` fixer.addMissingAtoms() File "/home/jkrieger/software/miniconda/envs/prody-github/lib/python3.9/site-packages/pdbfixer/pdbfixer.py", line 902, in addMissingAtoms (newTopology, newPositions, newAtoms, existingAtomMap) = self._addAtomsToTopology(True, True) File "/home/jkrieger/software/miniconda/envs/prody-github/lib/python3.9/site-packages/pdbfixer/pdbfixer.py", line 400, in _addAtomsToTopology self._addMissingResiduesToChain(newChain, insertHere, startPosition, endPosition, loopDirection, residue, newAtoms, newPositions, firstIndex)...

Applying deepres to a preprocessed version of EMD 21457 and then applying this protocol with a centered version of the corresponding PDB structure 6vyb, we get the B-factor as 0.000...

**Please briefly describe your suggestion.** It would be good to have a field about variants so they are easily searchable rather than just being plain text. **Please provide the schema...

Several of these are reviewed in https://pubmed.ncbi.nlm.nih.gov/32622329/ and I think they deserve a brief mention in your review too. I'm not sure how they fit into your categories Some of...

Installing using the spec file doesn't include healpy in the environment

2

**Describe the bug** Installing using the spec file doesn't include healpy in the environment. This gives the following error: ``` (opusdsd-0.3.2b) jkrieger@elnath ~/scipion3/software/em/opusdsd-0.3.2b (main) $ python -m cryodrgn.commands.preprocess -h Traceback...

Image size should be even error

28

**Describe the bug** Running preprocessing without --no-keep-real makes particles with 65 pixels instead of 64, and then train_cv for opusDSD complains that the pixel size isn't even. ``` Traceback (most...

fixes #1870 We may still need to remove or redo fetchPDBLigands, but everything should be fine for now This makes parsePDBLigand and PDBLigandRecord work now by using parseCCD: ``` In...

fix setup.py to copy hpb

1

This makes hpb work for Python 3.9 and 3.10 and doesn't break the install for Python 3.11 where hpb doesn't work I also added Karolina to the authors

mmCIF files often split different kinds of entities into chains and segments and have more divisions in the hierarchical view than PDB files For example, with 4ake, we get 4...

split pqr coords by line positions when needed

2

Potential fix for #1855 If the line does not have the right fields because of no spaces between coords to maintain pdb-like format, then it splits them by pdb-like positions