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
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
Very cool, that sounds ideal, I'll try it out!! Oli
On May 30, 2021, at 10:56 AM, Anthony James Schaefer <tony.schaefer@uga.edu> wrote:
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 <mailto:chimerax-users-bounces@cgl.ucsf.edu>> on behalf of Oliver Clarke <olibclarke@gmail.com <mailto:olibclarke@gmail.com>> Sent: Saturday, May 29, 2021 3:33 PM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto: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 <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <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
On Jun 1, 2021, at 9:44 AM, Tom Goddard <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
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
Okay, I have opened a request-for-enhancement ticket for this. --Eric
On Jun 8, 2021, at 11:10 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
This would be a great addition Eric!
Oli
On Jun 8, 2021, at 1:56 PM, Eric Pettersen <pett@cgl.ucsf.edu <mailto: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
participants (4)
-
Anthony James Schaefer -
Eric Pettersen -
Oliver Clarke -
Tom Goddard