[chimerax-users] How to hide a chain and overly the shown chain with another model

[Elaine Meng]

Hi Phil,
I don't know what residue numbers or chain IDs are in this structure, so can't say for certain how to hide it.  However your command only hides atoms, maybe you are trying to hide the ribbon? So if the chain ID you want to hide is C, you could try

hide /c target ar
...meaning target for hiding is atoms + ribbons
- or equivalently  -
hide /c atoms,ribbons

see "hide" help page
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/show.html>

Or to avoid having to know the chain ID, you could try to select the chain from the graphics window, say Ctrl-click to select a bit of it, then keyboard up arrow until the whole chain is selected (down arrow if you overshoot)

see selection help
<https://rbvi.ucsf.edu/chimerax/docs/user/selection.html#top>

... and then use command

hide sel targ ar

Presumably to add the other model you would just open it from file, or run the single-prediction and thus have it open automatically.  For overlay, you could try using the Matchmaker tool (menu: Tools... Structure Analysis... Matchmaker) or equivalently, the matchmaker command:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.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 Oct 13, 2022, at 3:47 PM, McClean, Phillip via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> I have a .pdb file obtained from ColabFold.  The model was developed with AlphaFold2 Multimer.  It has two chains.  How can I 1) hide only one chain and then 2) add a second model.  The second model will be the visualized chain developed only on its own.  I am looking for regions that might be different between the model with a second protein and by itself.
> 
> I tried
> 
> hide /c
> 
> but that didn't work.
> 
> Phil McClean