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@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@cgl.ucsf.edu> Sent: Friday, November 6, 2020 2:51:14 PM To: Rayna L. DeChance Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] help
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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@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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