[Chimera-users] saving PDB and saving maps

Elaine Meng meng at cgl.ucsf.edu
Tue Oct 23 08:51:58 PDT 2018

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”
Saving PDB
Saving after fitting

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.

I hope this helps,
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 at 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.

More information about the Chimera-users mailing list