Dear Alei Geng, Chimera reads SDF format. You could just open the SDF file of the ligands and open the PDB ffile of the receptor. However, even if you convert SDF to PDB in Chimera that should not change the coordinates. So you need to make sure you are opening the correct output file from DiffDock. I never used that program so I can't say anything more specific about it. 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 Nov 18, 2025, at 4:37 PM, galxj via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Dear Sir/Madam, I am a user of the Chimera software. I have obtained some molecular docking results from DiffDock, where the ligand molecules are in SDF format and the receptor protein is in PDB format. May I ask if it's possible to view the docking results using Chimera? I have tried many times but keep encountering errors. I also attempted to convert the SDF file to PDB format and opened both files together. Although both molecules are displayed, it is clear that the docking has not been performed correctly. Best Regards, Alei Geng