[Chimera-users] help

Elaine Meng meng at cgl.ucsf.edu
Fri Nov 6 12:51:14 PST 2020

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.

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


Alternatively you can just delete all the atoms you don't want before you save the file, e.g. with the "delete" command.

I hope this helps,
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>

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