Jan Kosinski

pdbx_PDB_ins_code, B_iso_or_equiv and other optional records should be optional in MMCIFParser.py

3

MMCIFParser.py requires mmCIF files to contain some optional atom_site records like pdbx_PDB_ins_code and B_iso_or_equiv. They are not required by the PDBx dictionary: https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_atom_site.pdbx_PDB_ins_code.html, https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_atom_site.B_iso_or_equiv.html and thus should be optional. The...

Modules missing when installing with conda

11

Hi, When I install with `conda create -n my_env -c conda-forge cctbx-base`, modules `probe`, `reduce`, and `chem_data` are not being installed. Is there a way of installing them in the...

Hi, For me `IMP.em.FitRestraint` is much slower with `use_rigid_bodies = True`, while the doc says it should be faster. For example, running `imp/modules/em/test/expensive_test_resample_by_rigid_bodies.py` test like this: `python -m unittest expensive_test_resample_by_rigid_bodies.Tests.test_resample`...

critical typo in kmeans.py (simport instead of import)

1

https://github.com/sokrypton/ColabDesign/blob/db689acfe3ee59b4fc0074115269aa0e4470eeec/colabdesign/seq/kmeans.py#L1

How to include post-translation modifications?

1

Hi, Is it possible to include post-translation modifications such as phosphorylation like in AlphaFold3?