Hi Daniel, I write the documentation, but wasn't sure what you mean by "Clip tool" and "Zone clipping tool"... Maybe you mean the mouse modes named "clip" and "zone"? The mouse modes are all documented here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#functions> (1,2) As it explains there, for "clip" mode, modifier keys allow moving the back instead of the front, or moving the whole slab. There is no default thickness but you can set a specific thickness with the "clip" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clip.html> There are Clipping preferences as to whether surface caps are shown and which kind of clipping the mousemode activates (the rotatable ones or the global ones that don't rotate). <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#clipping> (3,4) There is only limited control over the "zone" mousemode behavior: the "zone setting" command allows changing the label and background colors. The other behaviors of the mousemode are not customizable but you can use the "zone" command directly for some different behaviors: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/zone.html> As far as I knew you could not change the distance cutoffs in the "zone" mousemode. Trying what you said, I can somewhat get different values but it's hard to control and I'm not sure it is even supposed to work that way! Will consult with the person who wrote this function to see whether that was a bug or a feature. There is a "contour level" mouse mode to change volume contour level, in case you didn't see that already. (5) You can have both the rotatable and the nonrotatable clipping at the same time (see "clip" command) but as to whether you could consider one of them "extra" I do not know. It would not automatically narrow when you zoomed in, however. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clip.html> (6) It is debatable whether others would want the mouse mode to behave this way. Maybe one of the programmers on the team could advise on how you could alter the code in your download specifically to do this, or whether it is possible. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 27, 2024, at 1:07 AM, Daniel Larsson via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Ok, by trial-and-error I figured out the answer to question 3. One right-clicks and hold while dragging the mouse up/down to change the radius. I would much prefer to be able to set the contour-level by right clicking-and-hold and drag, since that is something one needs to change much more frequenly than the Zone radius. Also, I realize that Zone does not hide atoms outside of the sphere, so one has to hide atoms first and then zone will show the atoms inside of the sphere.
From: Daniel Larsson via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Reply to: Daniel Larsson <daniel.larsson@icm.uu.se> Date: Tuesday, 27 February 2024 at 09:42 To: "chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] right-mouse clipping
Hi all,
I have some question and comments regarding the very useful right-mouse Clipping tools. I feel they are poorly documented (or documentation is very difficult to find by Google searching).
For the Clip tool, it took me forever to realize how to “undo” the clipping (click again). The Zone clipping is a very nice feature, which shows atoms, residue labels and volume inside of an approximately 10 Å sphere and hides the volume and only show cartoon outside of the sphere. Right-clicking on the background hides the labels.
Some questions • How do I change the back/far clipping plane using the Clip tool (the icon suggests that you can clip into a slab)? • If so, is it possible to set a default thickness of that slab? • Is it possible to change the radius of the Zone clipping tool? • Is it possible to disable the cartoon outside of the sphere of the Zone clipping tool? • Alternatively have the ability to have an extra front clipping plane, which “intelligently” follows the camera when zooming in (hiding things closer to the centered region when zoomed in more)? • I use the mouse mode to center the view and camera pivot point (mousemode middleMode "center or translate"). It is possible to make the Zone clipping tool also center the view + pivot point so that I don’t have to also middle-click every time?
Regards, Daniel
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