Selecting residues in two chains
Hi Everyone, I have a .pdb file created using AF2 Multimer. It consists of two chains, B and C. Chain B is a protein with 315 residues, while Chain C is a protein with 662 residues. Each chain is modeled with structured and unstructured regions. I would like to only show residues 19-24 of Chain B and residues 1-190 of Chain C in the display window. I have tried using the information provided on the "Command-Line Target Specification" page, but I have not had any success with just displaying those ranges of residues in the display window. My goal is to highlight specific features of those ranges of residues to display their interaction. Thanks for any information you can provide. Phil McClean
Hi Phil, Maybe the problem is that you needed to hide the other stuff first? Here are some possible commands: hide target ar show /B:19-24 /C:1-190 target ar ...or if you only want to show atoms, not the ribbons, omit the "target ar" from the "show" command; in show/hide commands, target a is atoms (default), and target r or c is ribbons aka cartoons. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/show.html> The slash symbol indicates chain ID, and the colon indicates residue numbers or names: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#hierarchy> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 27, 2022, at 1:04 PM, McClean, Phillip via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Everyone,
I have a .pdb file created using AF2 Multimer. It consists of two chains, B and C. Chain B is a protein with 315 residues, while Chain C is a protein with 662 residues. Each chain is modeled with structured and unstructured regions. I would like to only show residues 19-24 of Chain B and residues 1-190 of Chain C in the display window.
I have tried using the information provided on the "Command-Line Target Specification" page, but I have not had any success with just displaying those ranges of residues in the display window. My goal is to highlight specific features of those ranges of residues to display their interaction.
Thanks for any information you can provide.
Phil McClean
Hi Elaine, Your suggestion worked to display just those parts of the two chains. I see that that for other actions, such has mlp, I also need to specify the residues. Thanks again for your help. Phil ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, October 27, 2022 4:20 PM To: McClean, Phillip <phillip.mcclean@ndsu.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Selecting residues in two chains Hi Phil, Maybe the problem is that you needed to hide the other stuff first? Here are some possible commands: hide target ar show /B:19-24 /C:1-190 target ar ...or if you only want to show atoms, not the ribbons, omit the "target ar" from the "show" command; in show/hide commands, target a is atoms (default), and target r or c is ribbons aka cartoons. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/show.html> The slash symbol indicates chain ID, and the colon indicates residue numbers or names: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#hierarchy> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 27, 2022, at 1:04 PM, McClean, Phillip via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Everyone,
I have a .pdb file created using AF2 Multimer. It consists of two chains, B and C. Chain B is a protein with 315 residues, while Chain C is a protein with 662 residues. Each chain is modeled with structured and unstructured regions. I would like to only show residues 19-24 of Chain B and residues 1-190 of Chain C in the display window.
I have tried using the information provided on the "Command-Line Target Specification" page, but I have not had any success with just displaying those ranges of residues in the display window. My goal is to highlight specific features of those ranges of residues to display their interaction.
Thanks for any information you can provide.
Phil McClean
Hi Phil, Many image-related commands (color, style, size) will not display what was currently hidden: for example, "color red" without specifying certain residues will make all the residues red but keep the hidden ones hidden. However, since "mlp" works on molecular surfaces, if you use it without specifying certain residues, it will create and display the whole surface of each protein chain. Elaine
On Oct 27, 2022, at 2:51 PM, McClean, Phillip via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Your suggestion worked to display just those parts of the two chains.
I see that that for other actions, such has mlp, I also need to specify the residues.
Thanks again for your help.
Phil From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, October 27, 2022 4:20 PM To: McClean, Phillip <phillip.mcclean@ndsu.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Selecting residues in two chains
Hi Phil, Maybe the problem is that you needed to hide the other stuff first? Here are some possible commands:
hide target ar show /B:19-24 /C:1-190 target ar
...or if you only want to show atoms, not the ribbons, omit the "target ar" from the "show" command; in show/hide commands, target a is atoms (default), and target r or c is ribbons aka cartoons. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/show.html>
The slash symbol indicates chain ID, and the colon indicates residue numbers or names: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#hierarchy>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 27, 2022, at 1:04 PM, McClean, Phillip via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Everyone,
I have a .pdb file created using AF2 Multimer. It consists of two chains, B and C. Chain B is a protein with 315 residues, while Chain C is a protein with 662 residues. Each chain is modeled with structured and unstructured regions. I would like to only show residues 19-24 of Chain B and residues 1-190 of Chain C in the display window.
I have tried using the information provided on the "Command-Line Target Specification" page, but I have not had any success with just displaying those ranges of residues in the display window. My goal is to highlight specific features of those ranges of residues to display their interaction.
Thanks for any information you can provide.
Phil McClean
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Hi Elaine, I just figured out this single command accomplishes the task: hide /B:1-18,125-315 /C:191-662 target ar I think I am starting to understand the nomenclature now. Again, thanks. Phil PS: I meant 124 not 24 in my previous email. My mistake. ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, October 27, 2022 4:20 PM To: McClean, Phillip <phillip.mcclean@ndsu.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Selecting residues in two chains Hi Phil, Maybe the problem is that you needed to hide the other stuff first? Here are some possible commands: hide target ar show /B:19-24 /C:1-190 target ar ...or if you only want to show atoms, not the ribbons, omit the "target ar" from the "show" command; in show/hide commands, target a is atoms (default), and target r or c is ribbons aka cartoons. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/show.html> The slash symbol indicates chain ID, and the colon indicates residue numbers or names: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#hierarchy> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 27, 2022, at 1:04 PM, McClean, Phillip via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Everyone,
I have a .pdb file created using AF2 Multimer. It consists of two chains, B and C. Chain B is a protein with 315 residues, while Chain C is a protein with 662 residues. Each chain is modeled with structured and unstructured regions. I would like to only show residues 19-24 of Chain B and residues 1-190 of Chain C in the display window.
I have tried using the information provided on the "Command-Line Target Specification" page, but I have not had any success with just displaying those ranges of residues in the display window. My goal is to highlight specific features of those ranges of residues to display their interaction.
Thanks for any information you can provide.
Phil McClean
participants (2)
-
Elaine Meng -
McClean, Phillip