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 <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/