Hello Vojo, First, consider whether you are using Chimera or ChimeraX. This email address is generally for asking ChimeraX questions. There is a different address for Chimera questions, chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> ... this time, however, I will answer for both programs so you do not need to send your question again. For both programs: Yes you can save your atomic structure after matching as a PDB file. ChimeraX: You can do it with the menu File... Save... as mentioned in the help: <https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#file> and in the resulting dialog choose file type PDB, and also for each model you are saving to a PDB file, make sure to turn on the option "Save relative to" and specify the same one for each of the matched structures, or else they will not be in the matched position. Alternatively you can do it with the "save" command making sure to include the "relModel" option, see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> Chimera: You can do it with the menu File... Save PDB, <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#menufile> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> again making sure to "Save relative to model" as explained above for ChimeraX. Alternatively you can do it with the "write" command with "relative" option, see: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> 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 May 13, 2026, at 6:42 PM, Vojo P Deretic via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Can you export results of your work in Chimera (for example after matching and aligning structure) as a .pdb file?

Vojo Deretic, Ph.D. Distinguished Professor Department Chair, MGM Director, AIM Center University of New Mexico School of Medicine vderetic@salud.unm.edu Follow AIM, NIH-funded Center of Biomedical Research Excellence: https://www.autophagy.center/ X/Twitter @AIM_autophagy Don’t forget to acknowledge the AIM Center (Autophagy, Inflammation and Metabolism) and the CoBRE grant in publications The AIM Center is supported by NIH grant P20GM121176. For citation options see suggested wording at https://www.autophagy.center/