Adding new modified aminoacids

Open andressanchezr4 opened this issue 6 months ago • 3 comments

I was using pdbfixer and found that some modified aminoacid-canonical aminoacid pairs were missing in the "substitution" dictionary. This threw errors when trying to run it. I fixed it just by adding these 3 to the dictionary in the pdbfixer.py:

'MLY': 'LYS' 'M3L': 'LYS' 'MLZ': 'LYS'

Jun 25 '25 12:06 andressanchezr4

Is your goal to add modified amino acids, or to replace them with canonical ones? The latest release can add anything found in the CCD.

Jun 25 '25 15:06 peastman

To replace them for the canonical, but I have a version from several months ago. Good to know that now this is being taken care of, thanks!

Jun 25 '25 16:06 andressanchezr4

The new version lets you add the modified residues, but not convert them to standard ones. I'll mark this as a feature request.

Jun 25 '25 16:06 peastman