[Chimera-users] help

[Elaine Meng]

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 at 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>