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 ________________________________ From: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Oliver Clarke olibclarke@gmail.com Sent: Saturday, May 29, 2021 3:33 PM To: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: [chimerax-users] Change default volume display settings?

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

Hi Oliver,

Currently ChimeraX does not have a way to save different volume display settings, like always using step 1. I'd like to add a command to do that. There is a "volume settings #3" command that reports the settings being used for a specific map. I've made a feature request for saving settings

https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4711

Also it would be interesting to add SEQCROW capability Tony Schaefer described to run certain commands when a model of a given type (volume, atomic structure) are opened to the ChimeraX core.

Tom

On May 29, 2021, at 12:33 PM, Oliver Clarke olibclarke@gmail.com wrote:

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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

This would be a great addition Eric!

Oli

On Jun 8, 2021, at 1:56 PM, Eric Pettersen pett@cgl.ucsf.edu wrote:

...

On Jun 1, 2021, at 9:44 AM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:

Also it would be interesting to add SEQCROW capability Tony Schaefer described to run certain commands when a model of a given type (volume, atomic structure) are opened to the ChimeraX core.

The SEQCROW capability is for models of a certain format (e.g., PDB, cube, Mol2), not type/class. Chimera had "New Molecules" and "New Surfaces" preference categories. I suppose ChimeraX could have a "New Models" settings category, with subsections for various model types, where you could specify commands to run when models of that type were opened.

--Eric

Eric Pettersen UCSF Computer Graphics Lab