Ah. The underscore. I forgot that ligand names with underscores have special code to do network lookups in the defunct PDB ligand expo. The workaround is to remove the underscore. And I'll finish the code to remove the lookup. For history, ligand names with underscores are only in names from the PDB for amino acids protonation variants. -- Greg On 7/15/2026 1:24 PM, Tom Goddard wrote:
Hi Ute,
The slow opening of AlphaFold 3 predictions with LIG_X residue codes does not appear to be because of failure to fetch templates. There is something very bad happening though. I tested opening an AF3 prediction of modest size 7800 atoms with 3 ligand residues codes LIG_A, LIG_B, LIG_C and it took an incredibly slow 60 seconds to open in the ChimeraX 1.12. If I renamed those 3 ligands to LIGAA, LIGBB, LIGCC, and restarted ChimeraX it opened in less than half a second. In both cases the ChimeraX Log reports it failed to fetch the ligand templates. Also if I open the LIG_A, LIG_B, LIG_C file a second time in the same ChimeraX session it opens is less than half a second.
Greg Couch wrote the ChimeraX mmCIF reader and hopefully he can investigate and fix it. I've attached my two example files for testing.
Tom
On Jul 15, 2026, at 2:40 AM, Ute Roehrig via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear All,
I am often opening AlphaFold 3 co-folding structures including small molecules in ChimeraX. In these models, ligands were provided as SMILES and are called LIG_X (with X being the chain label) in the AF3 output model.cif file. Opening these structures is very slow on my machine, because ChimeraX searches for a template for the ligands and finally fails with the warning "Unable to fetch template for 'LIG_X': will connect using distance criteria".
Is there any workaround? E.g. by telling ChimeraX not to look for a template?
Thank you for your help, Ute _______________________________________________ ChimeraX-users mailing list --chimerax-users@cgl.ucsf.edu To unsubscribe send an email tochimerax-users-leave@cgl.ucsf.edu Archives:https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/