FAQ: How do I change the shape of an unrecognized residue (flat, white hexagon)?

The easiest solution is to change the residue name in the PDB file to one that is already recognized by the script. Use any text editor to open the PDB file and modify the fourth column. Find and replace is useful, or use a substitution method via the command line (i.e. ‘sed‘ or ‘vi‘).

If this is a residue name that you are likely to encounter frequently, consider adding it to the list of residues within your script, as described in the Advanced Usage section.