Show density map only near center of view, like Coot

[olibclarke@…]

Oliver asks for map display only near center of view, the typical Coot display. Pymol has this as "roving density" mode. Also suggests being able to display side chains only near center of view, the Pymol capability being "roving detail".

Begin forwarded message:

From: Oliver Clarke
Subject: Re: [Chimera-users] Thoughts re enhancements for ChimeraX
Date: February 15, 2016 at 12:42:31 PM PST
To: Tom Goddard <goddard@…>

Hi Tom,

Another random thought for ChimeraX enhancements (take em or leave em as you like as usual):

Per model (or per representation) spherical clip around center of rotation:

This is to allow for one to look at a local portion of the density map in mesh, and have that portion update automatically upon centering. Implementing this in a per-model manner would also allow for the possibility of more complicated things - for example, to have a C-alpha trace always displayed, but show sidechains within 10 Å of the center of rotation. This would be fantastic for navigating around structures. For examples of the kind of thing I mean, load up pymol 1.8 and have a look at the demos "roving detail" and "roving density", or just have a look at the way Coot deals with maps.

At the moment, I do this kind of manually using the following alias:
# shows sphere of density of selected radius around center of rotation
# Usage: map_sphere radius
alias ^{map_sphere sel :unsel; ac mc; sop zone # sel $1; del sel; symclip $1
alias} map_sphere_off ~sop zone #

symclip is an alias I use for altering clipping symmetrically around the center of rotation:
# adjust clipping symmetrically around the center of rotation
#Usage: symclip
alias symclip cofr fixed; clip hither $1 fromCenter true; clip yon -$1 fromCenter true; cofr view

But a polished implementation would be a great help I think, maybe combined with a bare bones preset for looking at wireframe models in mesh maps, e.g. the following:

# shows sphere of density of selected radius around center of rotation
# Usage: map_sphere radius
alias ^{map_sphere sel :unsel; ac mc; sop zone # sel $1; del sel; symclip $1
alias} map_sphere_off ~sop zone #

Another thought - it might be worth considering making presets "special", non destructive modes, such that I could quickly switch for example to the hydrophobicity surface preset or the ribbons preset, and then easily switch the preset off and go back to what I had manually configured. This would enable briefly turning a preset on for analysis or navigation, then returning to the regular representation for figure making.

Cheers,
Oli.