Renaming atoms as per the remediation of atom names in peptide backbones

[keitaroyam]

Last month, atom names of several peptide(-like) monomers were updated https://www.wwpdb.org/news/news?year=2023#654a801dd78e004e766a96bd #39 #37.

Here 828 entries have been updated, and 202 entries no longer need aliases. Links and modifications have also been updated.

This was done using a custom made script in https://github.com/MonomerLibrary/Ligand-Tools/tree/main/fix-groups, without using AceDRG.

python rename_atoms.py ~/prog/monomers components.cif.gz  < monomer_list.txt 
python post_acedrg.py ~/prog/monomers/?/
python fix_monlib_list.py --monlib ~/prog/monomers

with monomer_list.txt prepared by @wojdyr, and components.cif.gz as of Dec 23, 2023.

Now these entries have _chem_comp_atom.alt_atom_id which store the old atom names. Refmacat and Servalcat can handle model files with the old names, thanks to gemmi (from 0.6.4).

Also, an unnecessary file (a/libcheck.lib) and unnecessary blocks (global and data) in some files have been removed.

[keitaroyam]

@drlemmus Could you run any tests using this branch?

[keitaroyam]

A bug in the script was fixed; actually 290 entries (instead of 202) no longer need aliases.

[drlemmus]

Tested and no errors found so far.

[keitaroyam]

Thank you Robbie. It seems good to me as well (just tested topology creation using gemmi, with affected pdb entries).