Add a command to set volume defaults

[olibclarke@…]

The following bug report has been submitted:
Platform:        macOS-13.4.1-x86_64-i386-64bit
ChimeraX Version: 1.7.dev202308222255 (2023-08-22 22:55:59 UTC)
Description
Oliver Clarke wanted to set volume defaults to always open volumes at step 1.  Need to add a command to set or save the volume defaults.

Log:
Could not find tool "Tabbed Toolbar"  
UCSF ChimeraX version: 1.7.dev202308222255 (2023-08-22)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 14989 format ccp4 fromDatabase emdb

Opened emdb 14989 as #1, grid size 448,448,448, pixel 0.862, shown at level
0.176, step 2, values float32  




OpenGL version: 4.1 ATI-4.12.7
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OpenGL vendor: ATI Technologies Inc.

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[Tom Goddard]

From: Oliver Clarke via ChimeraX-users <chimerax-users@…>
Subject: [chimerax-users] Change default step size for volumes?
Date: August 22, 2023 at 7:22:48 PM PDT
To: ChimeraX Users Help <chimerax-users@…>
Reply-To: Oliver Clarke

Hi,

Is there any way in ChimeraX to change the default step size for volumes?

There are volume commands (e.g. volume limitVoxelCount false) that look like they ought to do the trick but these only seem to apply to already opened volumes - is there a way to make it a persistent preference for newly opened volumes?

In Chimera this was a setting in the Volume Viewer, but I can’t find an equivalent yet in ChimeraX in either the global settings or the docs for the volume command.

Cheers
Oli

[Tom Goddard]

Fixed.

I added a new command "volume defaultvalues" that lets you set all the volume rendering options, and optionally save those defaults for future sessions. Here's an example for making all volumes display at step 1 and saving that for future settings

volume defaultvalues limitVoxelCount false saveSettings true

Here's an example to always show an outline box for volumes opened in the current session but not future sessions

vol def showoutline true

To see all the current default values use the command with no options

vol default

There is also a reset option to restore all the factory volume defaults:

vol default reset true

The options have the same names as with the "volume" command used for setting the rendering attributes for individual maps that are already opened.

Setting a new default value with the "volume defaultvalues" command will not change already opened maps. To change currently opened maps use the plain "volume" command.

Here is the full command syntax

volume defaultvalues [saveSettings true or false] [reset true or false] [dataCacheSize a number] [showOnOpen true or false] [voxelLimitForOpen a number] [showPlane true or false] [voxelLimitForPlane a number] [showOutlineBox true or false] [outlineBoxRgb a color] [limitVoxelCount true or false] [voxelLimit a number] [colormapOnGpu true or false] [colorMode colorMode] [colormapSize an integer] [colormapExtendLeft true or false] [colormapExtendRight true or false] [blendOnGpu true or false] [projectionMode projectionMode] [planeSpacing planeSpacing] [fullRegionOnGpu true or false] [btCorrection true or false] [minimalTextureMemory true or false] [maximumIntensityProjection true or false] [linearInterpolation true or false] [dimTransparency true or false] [dimTransparentVoxels true or false] [smoothLines true or false] [meshLighting true or false] [twoSidedLighting true or false] [flipNormals true or false] [subdivideSurface true or false] [subdivisionLevels an integer] [surfaceSmoothing true or false] [smoothingIterations an integer] [smoothingFactor a number] [squareMesh true or false] [capFaces true or false] [orthoplanes orthoplanes] [positionPlanes positionPlanes] [tiltedSlab true or false] [tiltedSlabAxis an axis vector] [tiltedSlabOffset a number] [tiltedSlabSpacing a number] [tiltedSlabPlaneCount an integer] [imageMode imageMode] [backingColor backingColor]

— set or report volume default values

colorMode: one of auto12, auto16, auto4, auto8, l12, l16, l4, l8, la12, la16, la4, la8, opaque12, opaque16, opaque4, opaque8, rgb12, rgb16, rgb4, rgb8, rgba12, rgba16, rgba4, or rgba8
projectionMode: one of 2d-x, 2d-xyz, 2d-y, 2d-z, 3d, or auto
planeSpacing: one of max, mean, or min or a number
orthoplanes: one of off, xy, xyz, xz, or yz
positionPlanes: some integers
imageMode: one of box faces, full region, orthoplanes, or tilted slab
backingColor: a color or none

[Tom Goddard]

I removed tiltedSlab, orthoplanes and imageMode options from the new volume defaultvalues command since those all control display style but they are not used for initial volume display style. Currently the initial volume display style is fixed (either surface or single plane image).