Showing atoms of select residues while also showing the remainder of the model
Hi Everyone,
I would like to show the atoms for just a few of the amino acid residues in a protein model will displaying the remainder of the model using the default format. Here is what I did:
1. Opened the model from my working directory 2. Selected a subset of residues using the select command: sel /A:102,105,106 3. Then used this command: show target a
This command gives me the atoms for all of the residues. Is there a way to just show the atoms for the selected residues while also leaving the remainder of the model in the standard format.
Thanks for any advice.
Phil McClean
Hi Phil, (A) Instead of command:
show target a
You could use command:
show sel target a
See the command help, where the "spec" shown in the usage can be several different things including the word "sel" to mean the current selection: https://rbvi.ucsf.edu/chimerax/docs/user/commands/show.html
(B) Alternatively, you could skip making the selection (your step 2) and specify the atoms directly in the show command:
show /A:102,105,106 target a
If you click the "spec" link in the command help, it goes to this other page describing the different ways to specify atoms, models, etc.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html
(C) yet other ways of acting on the current selection would be to
- click icons in the toolbar across the top, e.g. the "show atoms" icon that looks like phenylalanine sidechain sticks https://rbvi.ucsf.edu/chimerax/docs/user/tools/moldisplay.html
- use the Actions menu, e.g. Actions... Atoms/Bonds... Show https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#actions
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 9, 2023, at 2:51 PM, McClean, Phillip via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Everyone,
I would like to show the atoms for just a few of the amino acid residues in a protein model will displaying the remainder of the model using the default format. Here is what I did:
- Opened the model from my working directory
- Selected a subset of residues using the select command: sel /A:102,105,106
- Then used this command: show target a
This command gives me the atoms for all of the residues. Is there a way to just show the atoms for the selected residues while also leaving the remainder of the model in the standard format.
Thanks for any advice.
Phil McClean _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thanks Elaine,
I used your solution B with the command line. It work as I was hoping. BTW: I am liking the command line approach more and more. That way I better learn what Chimerax has to offer by doing that.
Phil ________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Thursday, March 9, 2023 5:25 PM To: McClean, Phillip phillip.mcclean@ndsu.edu Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Showing atoms of select residues while also showing the remainder of the model
Hi Phil, (A) Instead of command:
show target a
You could use command:
show sel target a
See the command help, where the "spec" shown in the usage can be several different things including the word "sel" to mean the current selection: https://rbvi.ucsf.edu/chimerax/docs/user/commands/show.html
(B) Alternatively, you could skip making the selection (your step 2) and specify the atoms directly in the show command:
show /A:102,105,106 target a
If you click the "spec" link in the command help, it goes to this other page describing the different ways to specify atoms, models, etc.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html
(C) yet other ways of acting on the current selection would be to
- click icons in the toolbar across the top, e.g. the "show atoms" icon that looks like phenylalanine sidechain sticks https://rbvi.ucsf.edu/chimerax/docs/user/tools/moldisplay.html
- use the Actions menu, e.g. Actions... Atoms/Bonds... Show https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#actions
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 9, 2023, at 2:51 PM, McClean, Phillip via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Everyone,
I would like to show the atoms for just a few of the amino acid residues in a protein model will displaying the remainder of the model using the default format. Here is what I did:
- Opened the model from my working directory
- Selected a subset of residues using the select command: sel /A:102,105,106
- Then used this command: show target a
This command gives me the atoms for all of the residues. Is there a way to just show the atoms for the selected residues while also leaving the remainder of the model in the standard format.
Thanks for any advice.
Phil McClean _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Great!
As a side note, if you use the Actions menu or the toolbar icons, ChimeraX will generate the corresponding command and show it in the Log... so those other approaches might also help in learning commands.
Best, Elaine
On Mar 9, 2023, at 3:29 PM, McClean, Phillip via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Thanks Elaine,
I used your solution B with the command line. It work as I was hoping. BTW: I am liking the command line approach more and more. That way I better learn what Chimerax has to offer by doing that.
Phil From: Elaine Meng meng@cgl.ucsf.edu Sent: Thursday, March 9, 2023 5:25 PM To: McClean, Phillip phillip.mcclean@ndsu.edu Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Showing atoms of select residues while also showing the remainder of the model
Hi Phil, (A) Instead of command:
show target a
You could use command:
show sel target a
See the command help, where the "spec" shown in the usage can be several different things including the word "sel" to mean the current selection: https://rbvi.ucsf.edu/chimerax/docs/user/commands/show.html
(B) Alternatively, you could skip making the selection (your step 2) and specify the atoms directly in the show command:
show /A:102,105,106 target a
If you click the "spec" link in the command help, it goes to this other page describing the different ways to specify atoms, models, etc.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html
(C) yet other ways of acting on the current selection would be to
- click icons in the toolbar across the top, e.g. the "show atoms" icon that looks like phenylalanine sidechain sticks
https://rbvi.ucsf.edu/chimerax/docs/user/tools/moldisplay.html
- use the Actions menu, e.g. Actions... Atoms/Bonds... Show
https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#actions
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 9, 2023, at 2:51 PM, McClean, Phillip via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Everyone,
I would like to show the atoms for just a few of the amino acid residues in a protein model will displaying the remainder of the model using the default format. Here is what I did:
- Opened the model from my working directory
- Selected a subset of residues using the select command: sel /A:102,105,106
- Then used this command: show target a
This command gives me the atoms for all of the residues. Is there a way to just show the atoms for the selected residues while also leaving the remainder of the model in the standard format.
Thanks for any advice.
Phil McClean _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (2)
-
Elaine Meng -
McClean, Phillip