Hi Rayees, I wasn't sure how you made the bild file. Using your own script? You can't really change the bild objects in ChimeraX after you open the bild file. Instead you would make another bild file that contains the colors and the object positions that you actually want and then open it. To flip the map, see command "volume flip" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#flip> Besides not allowing changing the objects in ChimeraX, another limitation of bild is that transparency is usually incorrect. If it is your own script making this bild file, you might consider using the shape command instead of bild format to create these geometric objects, see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html> The "shape" command creates surface models for which you can later modify the colors and transparency in ChimeraX if you want (e.g. using commands like "color" and "transparency" or the Actions menu). Still, when there is more than one transparent model in ChimeraX, they may be rendered incorrectly, see "Transparency and its limitations": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html#transparen...> Finally, there is nothing in the bild file that indicates the counts per bar, it only defines the length of the bar. So you would have to go back to whatever method was used to create that file to get the raw counts. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Jan 9, 2024, at 5:21 PM, Rayees Mattoo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi, I was trying to make an angular distribution plot using .bild file. I want to show the map inside the plot as in the attachment. Few questions:

-My map needs to be flipped to get the correct handedness, I think I need to flip the angular distribution plot as well, how to do that? or do I have to go back and get the .bild file for the flipped map?

-How can I change the colors and transparency of the angular distribution plot?

-Can I get the particle count for each cylinder in the plot? Wanted to show a scale bar for particle distribution around the sphere of the plot.

Best Rayees

Hi Elaine, is "another limitation of bild is that transparency is usually incorrect" a bug that should be fixed?     -- Greg On 1/9/2024 6:21 PM, Elaine Meng via ChimeraX-users wrote:

Hi Rayees, I wasn't sure how you made the bild file. Using your own script? You can't really change the bild objects in ChimeraX after you open the bild file. Instead you would make another bild file that contains the colors and the object positions that you actually want and then open it.

To flip the map, see command "volume flip" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#flip>

Besides not allowing changing the objects in ChimeraX, another limitation of bild is that transparency is usually incorrect. If it is your own script making this bild file, you might consider using the shape command instead of bild format to create these geometric objects, see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html>

The "shape" command creates surface models for which you can later modify the colors and transparency in ChimeraX if you want (e.g. using commands like "color" and "transparency" or the Actions menu). Still, when there is more than one transparent model in ChimeraX, they may be rendered incorrectly, see "Transparency and its limitations": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html#transparen...>

Finally, there is nothing in the bild file that indicates the counts per bar, it only defines the length of the bar. So you would have to go back to whatever method was used to create that file to get the raw counts.

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Jan 9, 2024, at 5:21 PM, Rayees Mattoo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi, I was trying to make an angular distribution plot using .bild file. I want to show the map inside the plot as in the attachment. Few questions:

-My map needs to be flipped to get the correct handedness, I think I need to flip the angular distribution plot as well, how to do that? or do I have to go back and get the .bild file for the flipped map?

-How can I change the colors and transparency of the angular distribution plot?

-Can I get the particle count for each cylinder in the plot? Wanted to show a scale bar for particle distribution around the sphere of the plot.

Best Rayees

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