[chimerax-users] [External] Re: Clip surface but not atoms

Mon Jul 27 12:16:02 PDT 2020

Thanks Elaine!  I’ll save the full string of commands you sent.

Tom’s guidance helped a lot - the figure came out just how I wanted it.

[DAC_binding_pocket_cutaway_good.png]

Thanks again -

M

On Jul 27, 2020, at 2:14 PM, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

Hi Miles,
In case it's useful, here's a little example that works in the current daily build.  This protein has oleic acid (residue name OLA) in a buried pocket.  The example turns off clipping for the parent model #1 (the atomic model, which includes any ribbon and atom/bond displays) but leaves it on for the molecular surface model #1.1.

open 1g74
surface
clip front 0 position :ola
clip model #!1 false
hide ~:ola target ar
style :ola ball

Probably you'd want to use the Right Mouse modes to translate and rotate the clipping plane interactively since it's hard to get the position you want with commands only.

Elaine

On Jul 25, 2020, at 7:12 AM, Pufall, Miles A <miles-pufall at uiowa.edu<mailto:miles-pufall at uiowa.edu>> wrote:

Cool - thanks!  Downloading now - will let you know if all is well.

Miles

On Jul 24, 2020, at 10:32 PM, Tom Goddard <goddard at sonic.net<mailto:goddard at sonic.net>> wrote:

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<mailto: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<mailto: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>

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