Hi Anas, This is not a bug: You cannot save a density map as PDB format, only the atoms. However, you do not need to save the map if you just save the atomic structure in the fitted position. Then you can just open the original map and your new PDB structure with the fitted atoms in the right position. To save the fitted position, in the “Save PDB” dialog, choose “Save models”: [your atomic model] and also the option “Save relative to model”: [your map model]. See “Saving Data” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html> Saving PDB <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> Saving after fitting <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting> If you want to save the map you can do it with Volume Viewer tool’s File menu, but the map formats do not include PDB. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#organization> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Oct 23, 2018, at 6:55 AM, Anas <anas.khawaja@ki.se> wrote:

The following bug report has been submitted: Platform: osx_x11 Chimera Version: (None given) Description Hello,

I am trying to superpose a .pdb file on a density map (.mrc), and save it as .pdb. Chimera saves the file, but when I open it it doesn’t display any density map. Just the pub file which was superposed. I am doing it to start model building, but I am stuck at this. Kindly help.