Hi Eleine and Tom,
Mea culpa! I completely overlooked that page. That page and your detailed feedback should most likely clarify my concerns. Thank you so much for your diligent work on ChimeraX software
as well as the documentation and support of it.
I will also consider using the ISOLDE plugin to inspect detailed map/model features.
Regards,
Daniel
From: Tom Goddard <goddard@sonic.net>
Date: Tuesday, 27 February 2024 at 19:29
To: Daniel Larsson <daniel.larsson@icm.uu.se>
Cc: "chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] right-mouse clipping
Hi Daniel,
Have you tried the ChimeraX ISOLDE plugin? For your task of inspecting regions of an atomic model and how well they fit to a map it may work better, as it is exactly intended to do that. The ChimeraX zone and clipping and centering mouse modes can also do that but those were not made specifically for that task, while ISOLDE was.
Googling chimerax mouse modes gave the top hit that has answers to most of your questions, so I am puzzled how you did not find it.
https://www.cgl.ucsf.edu/chimerax/docs/user/tools/mousemodes.html
Here are a few things I can add to Elaine's answers. For the most part mouse modes are not customizable. Depending on your way of using it you may not like the defaults. The cartoon is always shown for the Zone mouse mode. The reason is that it allows you to click on a nearby part of the ribbon to show a atoms, labels and mesh in a new region. Without the ribbon there would be nothing to click on to navigate to a new region centered outside your current zone region. If the ribbon is obstructing your view you may want to make it much thinner with the "cartoon style" command. I'm glas you found that the zone radius is changed by dragging -- that is the intended behavior and will be added to our documentation. There are no intelligent clip planes or extra front clip planes. If ChimeraX were a specialized visualization tool like Coot we might have such a thing, but it covers many molecular visualization needs so ChimeraX often does not have such specialized modes. ChimeraX does not by default use the click to set rotation center mode although it has a separate mode to do that. It has no ability to combine that mode with other modes like Zone so you can do multiple things in one click.
Tom