[Chimera-users] help

Elaine Meng meng at cgl.ucsf.edu
Fri Nov 6 12:55:35 PST 2020

One correction, use preset "Interactive 2" (not Interactive 1) to show all atoms.

> On Nov 6, 2020, at 12:51 PM, Elaine Meng <meng at 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 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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