Hello Ece, I could not reproduce this problem. I used model/refine loops on part of the protein chain in structure 2gbp with ligand glucose, and all of the output models included a copy of the glucose. Tested in version 1.17.3.

The documentation says that HET residues that are in the input model will be in the output model, and yes, that was what I observed. https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#building

However, you did not give much detail, and there are various possible reasons for your problem:

(1) ligand is not in the same model as the input protein structure. They should be together in the same model. If they are in separate models, you have to combine them into one model before using model loops. https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html

(2) ligand is not a HET residue. E.g. if your original input structure is in PDB format, the ligand coordinates should be in HETATM lines, not in ATOM lines. ATOM lines are used for standard amino acid and nucleic acid residues. (e.g. if the ligand is a peptide it is not a HET residue)

(3) when you save the output as a PDB file, make sure you are saving all the atoms of the model, not just the displayed or selected parts

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Apr 9, 2024, at 7:21 AM, Ecem Güngör via Chimera-users chimera-users@cgl.ucsf.edu wrote:

Hello all,

I have encountered an issue while working with a protein in complex with ligands. There are some missing regions in the protein structure, and I attempted to model these regions using the "Model/Refine Loops" tool in UCSF Chimera (version 1.17.3). However, I observed that when I saved the modeled structures as PDB files, the ligands were not included in the file. Additionally, in some models, the modeled C-terminal extended into the binding pocket in an unusual manner. I am curious whether this tool takes into account the presence of ligands or molecules in the structure while modeling missing regions. How can I prevent such issues from occurring? How can I model the missing long C-terminal in Chimera while ensuring that the presence of other ligands or molecules is also considered?

Thanks in advance. Ece.