The PDB got back to me and pointed out that the 12/12/2023 PDB News item, https://www2.rcsb.org/news/656f4404d78e004e766a96c6, explicitly states: "wwPDB has reserved a set of CCD IDs: 01 - 99, DRG, INH, LIG that will never be used in the PDB." So the long term solution will be to use "00", "01", etc. instead of LIG_0, LIG_1, .... And, ideally, add the chem_comp and chem_comp_bond mmCIF tables with the connectivity to the mmCIF file. -- Greg On 7/15/2026 1:28 PM, Greg Couch wrote:
Right now in ChimeraX, to avoid the network template lookup for ligands, you have two solutions: (1) use UNL for the component name for ligands with unknown connectivity, or (2) in a mmCIF file, give the connectivity with the chem_comp and chem_comp_bond tables. UNL comes from https://www.rcsb.org/ligand/UNL.
I agree that It is reasonable to have more component names avoid the network lookup. I will ask the PDB what they suggest to avoid problems in the future. But I will go ahead and add anything that starts with UNL optionally followed by an underscore or a digit. That will be in tomorrow's daily build.
-- Greg
On 7/15/2026 2:40 AM, Ute Roehrig via ChimeraX-users 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
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