Change default step size for volumes?
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
Hi Oli, There are ChimeraX settings equivalent to the ones in Chimera, e.g. "volume" command options "showOnOpen" and "voxelLimitForOpen", as well as the "voxelLimit" and "limitVoxelCount" that you mentioned. The latter two affect the step size: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling> However, as far as I know there isn't a way to save volume settings such as these in the preferences for persistence between sessions. You can add them as startup commands (Preferences, category: Startup): <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 22, 2023, at 7:22 PM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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
Thanks Elaine, Yes I found these and tried to add them as startup commands - there is no error, it seems like the commands are executed, but any new volume is still opened at step size 2 rather than 1. Cheers Oli
On Aug 23, 2023, at 12:01 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oli, There are ChimeraX settings equivalent to the ones in Chimera, e.g. "volume" command options "showOnOpen" and "voxelLimitForOpen", as well as the "voxelLimit" and "limitVoxelCount" that you mentioned. The latter two affect the step size:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling>
However, as far as I know there isn't a way to save volume settings such as these in the preferences for persistence between sessions. You can add them as startup commands (Preferences, category: Startup):
<https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 22, 2023, at 7:22 PM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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
Hi Oliver, There was no command to set the default rendering options when opening a volume. The volume command only operates on already open maps so won't do what you want. So I added a new command "volume defaultvalues" that allows setting defaults that will apply for one session and with a save option so they will apply to all future ChimeraX sessions. This will be in the ChimeraX daily build dated August 23, 2023. The command to always open volumes at step 1 (full resolution) no matter how large the file is and have that apply to all future sessions is volume default limitVoxelSize false save 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 (without saving, so it applies only to the current session) 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 <help:user/commands/volume.html#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
On Aug 23, 2023, at 9:03 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thanks Elaine,
Yes I found these and tried to add them as startup commands - there is no error, it seems like the commands are executed, but any new volume is still opened at step size 2 rather than 1.
Cheers Oli
On Aug 23, 2023, at 12:01 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oli, There are ChimeraX settings equivalent to the ones in Chimera, e.g. "volume" command options "showOnOpen" and "voxelLimitForOpen", as well as the "voxelLimit" and "limitVoxelCount" that you mentioned. The latter two affect the step size:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling>
However, as far as I know there isn't a way to save volume settings such as these in the preferences for persistence between sessions. You can add them as startup commands (Preferences, category: Startup):
<https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 22, 2023, at 7:22 PM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Ah that’s fantastic, thanks Tom! Will try it out tomorrow Cheers Oli
On Aug 23, 2023, at 9:15 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oliver,
There was no command to set the default rendering options when opening a volume. The volume command only operates on already open maps so won't do what you want. So I added a new command "volume defaultvalues" that allows setting defaults that will apply for one session and with a save option so they will apply to all future ChimeraX sessions. This will be in the ChimeraX daily build dated August 23, 2023. The command to always open volumes at step 1 (full resolution) no matter how large the file is and have that apply to all future sessions is
volume default limitVoxelSize false save 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 (without saving, so it applies only to the current session)
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 <help:user/commands/volume.html#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
On Aug 23, 2023, at 9:03 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thanks Elaine,
Yes I found these and tried to add them as startup commands - there is no error, it seems like the commands are executed, but any new volume is still opened at step size 2 rather than 1.
Cheers Oli
On Aug 23, 2023, at 12:01 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oli, There are ChimeraX settings equivalent to the ones in Chimera, e.g. "volume" command options "showOnOpen" and "voxelLimitForOpen", as well as the "voxelLimit" and "limitVoxelCount" that you mentioned. The latter two affect the step size:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling>
However, as far as I know there isn't a way to save volume settings such as these in the preferences for persistence between sessions. You can add them as startup commands (Preferences, category: Startup):
<https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 22, 2023, at 7:22 PM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Tom, I just tested this with the latest daily - works great, although I think it should be “limitVoxelCount”, not “limitVoxelSize”. Thanks this is very helpful! Cheers Oli
On Aug 23, 2023, at 9:15 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oliver,
There was no command to set the default rendering options when opening a volume. The volume command only operates on already open maps so won't do what you want. So I added a new command "volume defaultvalues" that allows setting defaults that will apply for one session and with a save option so they will apply to all future ChimeraX sessions. This will be in the ChimeraX daily build dated August 23, 2023. The command to always open volumes at step 1 (full resolution) no matter how large the file is and have that apply to all future sessions is
volume default limitVoxelSize false save 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 (without saving, so it applies only to the current session)
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 <help:user/commands/volume.html#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
On Aug 23, 2023, at 9:03 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thanks Elaine,
Yes I found these and tried to add them as startup commands - there is no error, it seems like the commands are executed, but any new volume is still opened at step size 2 rather than 1.
Cheers Oli
On Aug 23, 2023, at 12:01 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oli, There are ChimeraX settings equivalent to the ones in Chimera, e.g. "volume" command options "showOnOpen" and "voxelLimitForOpen", as well as the "voxelLimit" and "limitVoxelCount" that you mentioned. The latter two affect the step size:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling>
However, as far as I know there isn't a way to save volume settings such as these in the preferences for persistence between sessions. You can add them as startup commands (Preferences, category: Startup):
<https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 22, 2023, at 7:22 PM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (3)
-
Elaine Meng -
Oliver Clarke -
Tom Goddard