[chimerax-users] Clip surface but not atoms

[Tom Goddard]

Hi Miles,

  I added the ability to turn off clipping for specific models, in tonight's ChimeraX builds.  It only effects clip planes that rotate with the models, not the near / far camera clip planes:

	clip model #!1 off

The molecular surface of atomic model #1 is a submodel #1.1.  So I use "#!1" in this command instead of #1 so the command acts on only model #1 and not its child models #1.1, 1.2,...  You also will want to turn of surface caps

	surface cap false

so that the hole left in the clipped surface is not covered by a cap.

  Tom


> On Jul 24, 2020, at 11:35 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Miles!
> I remember meeting you at UCSF years ago.  I hope you are well.
> 
> This unfortunately is one of the features often needed for figures but that is not yet available in ChimeraX, the ability to clip one model (e.g. the surface) without clipping the other (e.g. the ligand atoms).  
> 
> I've listed it in the Missing Features section of the ChimeraX download page as "per-model clipping." It is one of the things on the To-Do list and is a ticket in our database.  I will add your e-mail address to the notification list for that ticket.  
> 
> For now, you would still need to use Chimera for per-model clipping.  Sorry about that,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Jul 24, 2020, at 10:32 AM, Pufall, Miles A <miles-pufall at uiowa.edu> wrote:
>> 
>> Hi!  
>> I’ve used Chimera for years (though not recently) and am switching to ChimeraX.  I’m looking to display the ligand binding pocket with the ligand, and the tutorial you have is great.  I generated this picture, which is really close to what I want.  It shows the ligand, and the pocket, and I’m able to slice it with the interactive side view tool to get to this point.  However, the left side of the ligand is slightly clipped. I’ve played with rotation and with moving the slice plane, but can’t find an orientation that shows the pocket so nicely (without any surface in the foreground) and not ligand clipping.  My question is: is there a way to tell ChimeraX to clip the surface but not the ligand?
>> Thanks!
>> Miles
>> 
>> <DAC_binding_pocket.png>
>> 
> 
> 
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
>