Common Issues

Contents

Ligand Code Conflicts with the CCD

Issue Description

The chemical component dictionary (CCD) has assigned codes to all small molecule and residues that appear in the PDB. RFD3 (via AtomWorks) can match these codes to their conformational structues in the CCD. However, and especially for enzyme design problems, the ligand structure you are using may be a transition state structure and will purposefully not match what is in the CCD. If this happens you will see several warning messages before the inference run crashes:

The shape mismatch error is how you know this particular issue is occuring.

Solution

You need to give your ligand a name that does not match any in the CCD. We recommend adding a colon or semicolon to the three-letter code, for example L:G. These characters render the code invalid for the CCD, so RFD3 will not try to match it to a known structure and instead use the structure from your PDB directly. You will need to update this label in both your input PDB/CIF file and your input JSON/YAML file.