Allow clip command distances specified from center of rotation

[olibclarke@…]

Current clip command specifies distances from center of bounding box. Oliver wants distances specified from center of rotation.

Begin forwarded message:

From: Oliver Clarke <olibclarke@…>
Subject: Re: [ChimeraX] #1646: Clip broken + depth cueing question
Date: January 28, 2019 at 2:06:34 PM PST
To: ChimeraX-bugs@…

...

I just want to clip in a slab either side of the center of rotation, which in Chimera used the fromCenter True option - would it be possible to add this option back to ChimeraX?

Cheers
Oli

[Tom Goddard]

The current clip command has many undesirable features. It interprets near/far relative to bounding box center if clip planes are not currently in use, but switches to relative motions if they are in use -- quite confusing. Also the near/far versus front/back terminology for view aligned versus model aligned planes is confusing. The command needs some redesign I think. Using the center of rotation as an origin seems ok, but it makes it hard to get a reproducible result.

[olibclarke@…]

The reason why I prefer to specify things relative to the center of rotation is so that I can keep the center of rotation locked to the center of view (which I do in Chimera using the alias cofron: "set showcofr; cofr view; clip on”), thereby allowing precise centering and navigation in a way that is otherwise not possible - it is easy to get a reproducible result via this method if the center of rotation is locked to the center of the view.

Cheers
Oli