[Chimera-users] Deleting residues from the structure

[Elaine Meng]

Hi Rayna, 
This seems like the same question you already asked.  One of the possibilities I gave you was to use the delete command, e.g.

delete :90-124

...if the numbering in the structure is the same as what you showed in the sequence window.

OR, you could use the mouse to drag a box in the sequence window, which will select on the structure, and then you could use command:

delete sel

You might want to try some of the tutorials if you want to become familiar with Chimera:

<https://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.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 13, 2020, at 12:56 PM, Rayna L. DeChance <rayna.dechance at wne.edu> wrote:
> 
> Hi Ms. Meng,
> Thank you again for the help! My research head and I had one more question, we opened the structure and visualized the sequence and we want to delete from 90-124 to match up our sequences of our protein. I attached an image of what we are trying to cut out. 
> Thank you again!
> Rayna DeChance
> Western New England University 
> Student 
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Friday, November 6, 2020 2:51:14 PM
> To: Rayna L. DeChance
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] help
>  
> The External Email below originated from outside the University. Unless you recognize the sender, do not click links, open attachments, or respond.
> 
> 
> 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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