Allow saving default volume display settings

[olibclarke@…]

Begin forwarded message:

From: Oliver Clarke
Subject: [chimerax-users] Change default volume display settings?
Date: May 29, 2021 at 12:33:28 PM PDT
To: ChimeraX Users Help <chimerax-users@…>

Hi,

Is there any way in ChimeraX to change default volume display settings? For example, I would like to set all volumes to "step 1" by default - in Chimera I can set these defaults in the Volume Viewer menu but I can't see an equivalent in ChimeraX.

Sort of related - I wonder if it would be possible to have the option to set default display preferences for molecules or maps? Or more generally, have a script that executes when a file of a particular type is loaded - similar to how the startup commands are executed when ChimeraX is started, but triggered by the opening of a particular filetype and applied to that particular model?

Cheers
Oli

[Tom Goddard]

Tony Schaefer described a related capability of running commands when a model of a specific type is opened.

Begin forwarded message:

From: Anthony James Schaefer
Subject: Re: [chimerax-users] Change default volume display settings?
Date: May 30, 2021 at 7:56:25 AM PDT
To: Oliver Clarke , ChimeraX Users Help <chimerax-users@…>

Oliver,

SEQCROW might be able to help with your second question. If you go to Favorites/Preferences -> Settings... -> SEQCROW tab (you will have to restart ChimeraX after installing SEQCROW to see this), one of the options is 'commands to execute when a model is added'. You can prefix the command with a file type and use <model> in place of the model's ID. For example:

cub,cube: volume <model> level -0.018 level 0.018 color red color blue; trans <model> 50
cif: color <model> blue

will execute that volume command whenever a *.cub or *.cube file is opened and will color all *.cif models blue. Currently SEQCROW guesses the file type using the model's "filename" attribute, which isn't always set. It will also fire if the model name starts with "ext:" (e.g. "smiles:"). I've recently learned of a more accurate way to figure out the file type (thanks Eric!) which I'll use in the next version of SEQCROW.

Hope that helps,

Tony