Hi Emily, I changed the subject line to be more descriptive for archive purposes. You can combine models (sets of atoms opened from separate files, for example) using the "combine" command. As explained in the help, you could try using "combine" with "retainIds true" if the chain IDs and numbering in the original models wouldn't give multiple residues with both the same ID and number: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> However, this will not add bonds. The model has to be combined before you can add bonds, see "bond" command and/or Build Structure tool: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html> So if the models already have the appropriate spatial relationships, I imagine combining them and then adding the necessary bonds. But you might need to change chain IDs and/or residue numbering in the original models before combining them to allow using "combine" with "retainIds true". There is also another approach, see Join Models in Build Structure or command "build join". This combines two models at the same time as forming a bond with specified length and angles, which would also move & reorient one of the models. However, it may be difficult to specify the bond length and angles correctly to get the desired spatial relationship, so if you already had that, I'd suggest simply using "combine" instead. 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 Oct 29, 2025, at 2:38 PM, Emily Cioppa via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Good evening, In addition to my previous question, I am also having difficulty appending chains. If I import molecular models into Chimera/ChimeraX that each have individual model names and singular Chain IDs, is there a way to combine these into a singular model and renumber the residues as one continuous sequence throughout the combined model? For example, I have three molecular models that are each components of a single RNA molecule, and each have their own pdb file and a singular Chain ID. I know how to physically orient all of them spatially and renumber the residues of each such that when hovering over the molecular model moving from 5’ to 3’ the sequence numbering is continuous and correct across all chains. However, even when I combine the three individual models into one at the beginning and change the chain IDs of all three to be the same ID at the end, when I view the combination model in sequence viewer, it has just appended all three chains together with no regard to ! residue order. Since each of the three models is a chunk of double helix, I would need the numbering to be in 5’ to 3’ order throughout the entire combination model sequence viewer, in the way that I have renumbered it and in the way that it is in the visible combined model/structure. Thank you for your help.