Hi Mahesh, In ChimeraX, the way to move only specific atoms or certain models is by using mouse modes assigned to those functions. I.e. you could select some part of one model (many ways, one is a command like: select #1) and then assign right mouse button to move only selected models. Similarly, there is a mouse mode to move only selected atoms. If you look in the Right Mouse tab of the toolbar across the top, there are many icons for assigning the function of the right mouse button (or touchpad equivalent). Or, you can use the "mousemode" command to assign the function to other buttons or button combinations. See "selection" which is (by default) indicated with green outlines: <https://rbvi.ucsf.edu/chimerax/docs/user/selection.html> See "selective manipulation" which discusses mouse modes for moving only some part of the atoms that you have open: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#selective> See Right Mouse toolbar, discussion of trackpad equivalent depending what kind of computer you have: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> See "mousemode" command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> Specifically regarding forming a multimer from a monomer, some (but not all) PDB files already contain the necessary information so that you would not have to create it manually. As you said, the manual way is to open the same structure multiple times and manually position the copies. However, if the file already contains the symmetry information you may be able to generate the multimer with "sym" ... for example, commands: open 1o22 sym #1 assembly 1 copies true See "sym" command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#assembly> 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 Jan 3, 2025, at 7:18 AM, Mahesh Chandrasekharan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi: First up, thank you and your team for all your efforts in creating and maintaining Chimera and ChimeraX. They are an awesome tool/package!

It would be very helpful if you could please assist me with the two questions below. 1) I have a PDB downloaded from Alphafold. I would like to ‘drag out’ or reposition regions in order to enable their better visualization for a figure that I need for a grant. How can I select and reposition specific regions of a protein structure in ChimeraX?

2) The protein of my interest is a homodimer. I would like to open two copies of the relevant PDB file and manipulate them as two separate proteins. I have made a duplicate and relabeled the PDB file. However, when I open it ChimeraX along with the original, the two files seem linked, and I am unable to work on them separately. Is there a way to open two copies of the same PDB file to ‘recreate’ a homodimer?

Thank you, Best, Mahesh