Dear Xuemei Yang, The initial display (how it looks when you first open the structure) does not show all atoms. It tries to make a convenient default display that is easier to view than all atoms, using rules like only showing small-molecule ligands and nearby atoms: <https://rbvi.ucsf.edu/chimerax/docs/user/autostyle.html> However, unless there is some other problem, you can display the lipids after you open the file. For example, show show residues named QSR, command: show :QSR ...Or, you could show all atoms, but then it may be hard to see where the lipids are. Example command to show all atoms as sticks: preset sticks If it still does not show, maybe there is some other problem like the format of the residue in the PDB file. If so, you would need to send us an example PDB file to figure it out. I see that PDB 6v8q contains a cardiolipin derivative named QSR, but it is already automatically displayed when I open the file. 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 Aug 8, 2024, at 4:42 AM, 杨雪梅 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX support group,

When I open my PDB with ChimeraX, some lipids (get from the coot library with three-code) could not be seen. When it open with pymol, the lipids were displayed normal. Have you met such problem and how did you fix it?

Looking forward to your kind help.

Sincerely yours,

Xuemei Yang

Chinese Academy of Sciences Shanghai Institute of Materia Medica