thank you very much, Elaine! On 9/8/21, 11:43 AM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote: Hi Bingchun, The "combine" command is only in the daily build. It was added after release 1.2. No idea what you mean by only partial files saved. The "save" command or menu File... Save will save all of the atoms if you don't use the "displayed only" or "selected only" options. If not, you could use Help... Report a Bug and attach your session and say exactly what save options you used on that session and why you think part of the result is missing. Just use the "save" command or menu File... Save and choose PDB format and one of your atomic models, and make sure to use the option to save "relative to" the map model. You could do that twice to get two new PDB files see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> If you wanted both of your original atomic models in only one PDB file, it may be best to combine them into a single model first. E.g. use the command "combine" (requires recent daily build, is not in version 1.2) on the two pdb models to make a new combined model. For example, combine models #2,3 to make a new model #5: combine #2,3 modelId #5 name mynewmodel see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> ...then use either the "save" command or menu File... Save as above to save the new model relative to the map. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 8, 2021, at 7:02 AM, Zhao, Bingchun (NIH/VRC) [F] via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: > > Hi, > First, I wanna thank you for all your work to develop ChimeraX, it’s so powerful. > > I do have a question and would like to have your input. > > I opened a EM density map (.mrc) and two pdb files in chimerax (version 1.2), then fit all the pdb models into the EM map. > Then, I hide the EM map, only show the pdb models after fitting, and then I would like to save these all pdb files in a new pdb file with all position information after fitting. > > Would you please give me any direction how to do this? > > I tried saving them, but only partial pdb files saved, also tried combine commend, but it said no such commend. > > Thank you very much! > Best, > bingchun