[chimerax-users] Useful tools ideas/requests

[Tom Goddard]

Hi Shayne,

  Oh you want a frame counter or frame time in your movie recording.  That makes more sense.  That can be done with the ChimeraX perframe command.  Here is an example showing how on the ChimeraX recipes web site.

	https://rbvi.github.io/chimerax-recipes/movie_time/movie_time.html <https://rbvi.github.io/chimerax-recipes/movie_time/movie_time.html>

  Tom



> On Oct 21, 2022, at 10:59 AM, Shayne Quinn <shayne.quinn at mines.sdsmt.edu> wrote:
> 
> Awesome, thank you so much the axes are exactly what I am looking for as well as the coverslip idea! I realized I was a little unclear on the time stamp comment. I was wondering if there was something for timestamping Vseries data to apply a changing timestamp to each frame of a movie.
> 
> On Thu, Oct 20, 2022 at 8:12 PM Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
> Hi Shayne,
> 
>   Thanks for the suggestions.  I made some example Python code that defines ChimeraX commands to make the colored outline box, the coverslip slab, and a timestamp label.
> 
> 	https://rbvi.github.io/chimerax-recipes/lightsheet/lightsheet.html <https://rbvi.github.io/chimerax-recipes/lightsheet/lightsheet.html>
> 
> Maybe some improved version of the colored axes and timestamp command will some day go into ChimeraX.  I made a feature request for the color axes which I think might be of interest to others.
> 
> 	https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7832 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7832>
> 
>   Tom
> 
> <lightsheet.png>
> 
>> On Oct 19, 2022, at 12:01 PM, Shayne Quinn via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>> 
>> Hello,
>> I have been using ChimeraX for a few years now for multidimensional cell bio-imaging and cannot thank the team and developers enough for such an amazing program. I am not sure where to ask for other useful tools so I am starting here. These may already exist but I was unsuccessful in finding them in the user guide so my apologies if I missed them.
>> 
>> 1) Is there an option to color the different axis for the 'showOutlineBox' feature for volumes?
>>      For example box lines in x-blue, y-green and z-red to help keep orientation
>>      (I have included a mock version in the attachment)
>> 
>> 2) I work specifically with Lattice Light Sheet Data which requires our 3D cells to be placed on glass coverslip that do not show up in the captured data but are useful for referencing orientation. Is there a feature in place already that would allow me to create a mock coverslip. 
>>      So far I resorted to importing a throwaway volume (Volume 4 in attachment) and made the threshold for a surface ~0, set it to grey, and made it fill the bottom 5 pixels or so, shown in the attachment.
>> 
>> 3) Is there a time stamp feature similar to the scale bar function that has already been implemented?
>> 
>> Thank you so much for all the time and effort that has been put in and for creating such an amazing visualization tool!
>> 
>> Cheers,
>> Shayne Quinn
>> <Chimera Session.PNG>_______________________________________________
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