Hi Dorien, ChimeraX is not able to apply scene clip planes at different positions to different models. You can only turn off clipping by scene clip planes for specific models as you already discovered. You could use a scene clip plane to see your ligand bound to the blue protein, then turn off clipping on for the brown protein and use the near clip plane to cut away the frontmost part of the brown protein. The easiest way to try to get the right view would be to use the Side View tools, menu Tools / General / Side View and drag the left yellow line representing the front clip plane to change the clip depth. Then rotate your view around to see if you can get the effect you are looking for. A few unrelated suggestions. 1) Your brown protein and blue protein seem to severely clash, as shown by the clip surface where the brown and blue are interspersed -- it seems like something is wrong with your protein positions or docking. 2) I think making the blue and yellow proteins fully opaque would give better lighting of the binding site. 3) All the loops of the brown AlphaFold model (known as "barbed wire") are likely just disordered. Unless you are making a point about the disordered part you might exclude them. Tom

On Oct 24, 2023, at 1:12 AM, Dorien Pastoors via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

Thanks for maintaining such a nice software package! I’m still learning, and I’m currently stuck on clipping. I’m trying to clip models differently in ChimeraX. My aim is to have a global clipping plane to visualize two drugs binding to two domains (in the image in yellow/blue). Now I would like to offset the clipping plane slightly for surrounding protein (in beige). I would like to do this to increase the depth in my image and to emphasize that these domains are embedded in a bigger protein. As it is in fact a huge protein (its an alphafold predicted structure) making the entire protein transparent will still obscure the view on the compounds in their domains. As you can see, by using clip model I’ve been able to turn off clipping for the drugs in their binding pockets. However, with clip model I can only switch on or off the entire clipping plane , not offset it for a particular model.

I’ve tried: clip model #2.3 front -10 clip model #2.3 offset -10 With clip model I can’t specify an offset as it gives an error, I can only turn clipping off completely with “clip model #2.3 false”, while “clip front -10” affects the total clipping plane, and I cannot specify a particular model for this clipping plane. (the beige protein model is #2.3)

Hope this is clear enough and you have a solution! Thanks in advance!

Kind regards,

Dorien Pastoors

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