Did you uncheck 'use untransformed coordinates' checkbox before saving? On Tue, Oct 25, 2016 at 10:21 PM, gutta ramadevi <ramadevi364@yahoo.co.in <mailto:ramadevi364@yahoo.co.in>> wrote: Good day, I am using chimera following tutorials. I saved the processed receptor and ligand files in pdb format.But the files are not being saved.when i open the saved files i am getting the unprocessed receptor and ligand files. please help me to save the files. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> -- Dr. Subha Kalyaanamoorthy Post Doctoral Fellow Faculty of Pharmacy and Pharmaceutical Sciences University of Alberta Edmonton, Canada.