One correction, use preset "Interactive 2" (not Interactive 1) to show all atoms.
On Nov 6, 2020, at 12:51 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Rayna, In the Save PDB dialog (menu: File... Save PDB), there are options to "Save only displayed atoms" or "Save only selected atoms."
First show all the atoms, so you can actually see what is there, e.g. menu: Presets... Interactive 1 (all atoms). Then either select the ones you want or hide the ones you don't want. Then in the Save PDB dialog turn on the appropriate option. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
You can select with the mouse (Ctrl-click/drag) or with the "select" command. In the command you can specify model number, ranges of residue numbers, etc., for example:
select #3:45-83,90-98
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>
Alternatively you can just delete all the atoms you don't want before you save the file, e.g. with the "delete" command. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 6, 2020, at 11:58 AM, Rayna L. DeChance <rayna.dechance@wne.edu> wrote:
Hi, I was wondering if you knew how to cut out (clip) a part of the protein and save the remaining part as a PDB file. I attached the file I was working with that has the two proteins that are aligned together and we want only a certain part of this alignment to be clip. Thank you <session 1.py>
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users