Re: [chimerax-users] Mercator projection of MRC voluem coloured by attribute

[goddard@…]

Hi Pranav,

  I guess you mean you want to save a 360 degree projection image of your colored map?  There is nothing quite like that in ChimeraX.  If you want a 360 view from the center of the map you can get that with "camera 360" after positioning the view point in the middle of the map.  For example

	open 1080 from emdb
	color cylindrical #1 palette redblue
	move z 350
	turn x 90 center #1
	camera 360

There is also command volume unroll that can unroll a cylindrical map.  But it does not preserve coloring.  And there was a flatten icosahedron capability that worked with atomic models in Chimera that is not in ChimeraX.

	https://www.cgl.ucsf.edu/chimera/experimental/flatten_icosahedron/flaticos.html

For what you want you could spin the model around 360 degrees recording images each 0.2 degree, then have a script take the center column of pixels from each image and lay those columns side-by-side in a single image 1800 pixels wide.

  Tom

Example of camera 360 giving view inside map EMDB 1080.


> On Oct 22, 2024, at 10:51 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
> 
> hi Team,
> This is potentially a left-of-center question, but is there a way I
> could generate a mercator projection of an MRC volume that I have
> colored by zone? I am happy to code this up in the chimerax python
> environment, but I am not sure how I could access the voxel colour
> information before projecting the volume.
> 
> Best,
> Pranav
> --
> Pranav Shah
> Postdoctoral Research Fellow.
> 
> Division of Structural Biology,
> Wellcome Trust Centre for Human Genetics,
> University of Oxford,
> Roosevelt Drive, Oxford OX3 7BN,
> UK
> _______________________________________________
> 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/
> 

[goddard@…]

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[Tom Goddard]

Handled on ChimeraX mailing list.

[pranav.shah@…]

Love it! Thanks Tom, this might just work. WOuld you be happy to share the script you used to generate that stretched out view?


Best,
Pranav
--
Pranav Shah
Post-doctoral Research Associate (PDRA)
Division of Structural Biology (STRUBI)
University of Oxford.
Center for Human Genetics,
Roosevelt Drive,
Oxford, OX3 7BN, UK

________________________________________
From: Tom Goddard <goddard@sonic.net>
Sent: 22 October 2024 20:19
To: Pranav Shah
Cc: ChimeraX-bugs@cgl.ucsf.edu
Subject: Re: [chimerax-users] Mercator projection of MRC voluem coloured by attribute

Hi Pranav,

  I guess you mean you want to save a 360 degree projection image of your colored map?  There is nothing quite like that in ChimeraX.  If you want a 360 view from the center of the map you can get that with "camera 360" after positioning the view point in the middle of the map.  For example

open 1080 from emdb
color cylindrical #1 palette redblue
move z 350
turn x 90 center #1
camera 360

There is also command volume unroll that can unroll a cylindrical map.  But it does not preserve coloring.  And there was a flatten icosahedron capability that worked with atomic models in Chimera that is not in ChimeraX.

https://www.cgl.ucsf.edu/chimera/experimental/flatten_icosahedron/flaticos.html

For what you want you could spin the model around 360 degrees recording images each 0.2 degree, then have a script take the center column of pixels from each image and lay those columns side-by-side in a single image 1800 pixels wide.

  Tom

Example of camera 360 giving view inside map EMDB 1080.
[emd1080.png][emd1080_360.png]

On Oct 22, 2024, at 10:51 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

hi Team,
This is potentially a left-of-center question, but is there a way I
could generate a mercator projection of an MRC volume that I have
colored by zone? I am happy to code this up in the chimerax python
environment, but I am not sure how I could access the voxel colour
information before projecting the volume.

Best,
Pranav
--
Pranav Shah
Postdoctoral Research Fellow.

Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive, Oxford OX3 7BN,
UK
_______________________________________________
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/

emd1080-1.png​

emd1080_360-1.png​

[pranav.shah@…]

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[pranav.shah@…]

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