[Chimera-users] help

Rayna L. DeChance rayna.dechance at wne.edu
Fri Nov 13 12:56:19 PST 2020

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


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.

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>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20201113/bf271f24/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screen Shot 2020-11-13 at 3.55.19 PM.png
Type: image/png
Size: 161511 bytes
Desc: Screen Shot 2020-11-13 at 3.55.19 PM.png
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20201113/bf271f24/attachment-0001.png>

More information about the Chimera-users mailing list