[chimerax-users] Selecting residues in two chains

[Elaine Meng]

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 at 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 at cgl.ucsf.edu>
> Sent: Thursday, October 27, 2022 4:20 PM
> To: McClean, Phillip <phillip.mcclean at ndsu.edu>
> Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at 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 at 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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