Do you have a tutorial for ChimeraX generating publication quality surface and mesh maps with a docked model, please?
Thanks
Dr Mark F Rosenberg
Hello Mark, If by "docked model" you mean an atomic model fitted into a map, no, there isn't a tutorial specifically about making a figure of that.
However, we have several example images along with the command scripts that were used to generate them, including at least two images that are surfaces with structures inside: https://www.rbvi.ucsf.edu/chimerax/gallery.html
... and numerous multi-step tutorials, including https://www.rbvi.ucsf.edu/chimerax/tutorials.html
...intro to cryoEM maps + structures https://www.rbvi.ucsf.edu/chimerax/data/stanford-apr2022/cryoem_intro.html
...movie-making with cryoEM data https://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/cryomovie.html
... ways to display/analyze ligand-protein binding sites https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html
In ChimeraX, generally what you see is what you get in the image, so you can just try coloring, lighting and style commands (many of which you can run simply by clicking icons in the toolbar, or using the Actions menu) until you like what you see.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 20, 2023, at 4:29 AM, Mark Rosenberg via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Do you have a tutorial for ChimeraX generating publication quality surface and mesh maps with a docked model, please?
Thanks
Dr Mark F Rosenberg
Hi Elanie,
I have an atomic model fitted into the map. I was looking for instructions on improving the mesh's representation with the docked atomic model.
Thank you. That was very helpful.
Kind Regards
Mark ________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Monday, November 20, 2023 4:21 PM To: Mark Rosenberg mark.rosenberg@manchester.ac.uk Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Tutorial
Hello Mark, If by "docked model" you mean an atomic model fitted into a map, no, there isn't a tutorial specifically about making a figure of that.
However, we have several example images along with the command scripts that were used to generate them, including at least two images that are surfaces with structures inside: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/gallery.html_... [rbvi[.]ucsf[.]edu]>
... and numerous multi-step tutorials, including <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/tutorials.htm... [rbvi[.]ucsf[.]edu]>
...intro to cryoEM maps + structures <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/data/stanford... [rbvi[.]ucsf[.]edu]>
...movie-making with cryoEM data <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/data/sbgrid-ap... [rbvi[.]ucsf[.]edu]>
... ways to display/analyze ligand-protein binding sites <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/docs/user/tut... [rbvi[.]ucsf[.]edu]>
In ChimeraX, generally what you see is what you get in the image, so you can just try coloring, lighting and style commands (many of which you can run simply by clicking icons in the toolbar, or using the Actions menu) until you like what you see.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 20, 2023, at 4:29 AM, Mark Rosenberg via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Do you have a tutorial for ChimeraX generating publication quality surface and mesh maps with a docked model, please?
Thanks
Dr Mark F Rosenberg
Hi Mark,
Take a look at the section "Inspecting side-chain density using zones" in this ChimeraX tutorial
https://www.rbvi.ucsf.edu/chimerax/data/stanford-jul2019/tutorial2.html
It talks about how to show the density mesh around side chains to clearly show the quality of the map.
Tom

On Nov 20, 2023, at 9:06 AM, Mark Rosenberg via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Elanie,
I have an atomic model fitted into the map. I was looking for instructions on improving the mesh's representation with the docked atomic model.
Thank you. That was very helpful.
Kind Regards
Mark From: Elaine Meng <meng@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> Sent: Monday, November 20, 2023 4:21 PM To: Mark Rosenberg <mark.rosenberg@manchester.ac.uk mailto:mark.rosenberg@manchester.ac.uk> Cc: chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Tutorial
Hello Mark, If by "docked model" you mean an atomic model fitted into a map, no, there isn't a tutorial specifically about making a figure of that.
However, we have several example images along with the command scripts that were used to generate them, including at least two images that are surfaces with structures inside: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/gallery.html_... [rbvi[.]ucsf[.]edu] https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/gallery.html__;!!PDiH4ENfjr2_Jw!HhAqMVRYlcC2fo-2BxbDo0-TdAEOTcUmT5jSa9ECRyUQVfrcBwTnTI9Qu1UQj3ATeyaC-AjnlPu0c_Z7VQxFidVDdu0$%20[rbvi[.]ucsf[.]edu]>
... and numerous multi-step tutorials, including <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/tutorials.htm... [rbvi[.]ucsf[.]edu] https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/tutorials.html__;!!PDiH4ENfjr2_Jw!HhAqMVRYlcC2fo-2BxbDo0-TdAEOTcUmT5jSa9ECRyUQVfrcBwTnTI9Qu1UQj3ATeyaC-AjnlPu0c_Z7VQxFR_kSbP8$%20[rbvi[.]ucsf[.]edu]>
...intro to cryoEM maps + structures <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/data/stanford... [rbvi[.]ucsf[.]edu] https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/data/stanford-apr2022/cryoem_intro.html__;!!PDiH4ENfjr2_Jw!HhAqMVRYlcC2fo-2BxbDo0-TdAEOTcUmT5jSa9ECRyUQVfrcBwTnTI9Qu1UQj3ATeyaC-AjnlPu0c_Z7VQxFN518WzE$%20[rbvi[.]ucsf[.]edu]>
...movie-making with cryoEM data <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/data/sbgrid-ap... [rbvi[.]ucsf[.]edu] https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/cryomovie.html__;!!PDiH4ENfjr2_Jw!HhAqMVRYlcC2fo-2BxbDo0-TdAEOTcUmT5jSa9ECRyUQVfrcBwTnTI9Qu1UQj3ATeyaC-AjnlPu0c_Z7VQxFXeKFqUE$%20[rbvi[.]ucsf[.]edu]>
... ways to display/analyze ligand-protein binding sites <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/docs/user/tut... [rbvi[.]ucsf[.]edu] https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html__;!!PDiH4ENfjr2_Jw!HhAqMVRYlcC2fo-2BxbDo0-TdAEOTcUmT5jSa9ECRyUQVfrcBwTnTI9Qu1UQj3ATeyaC-AjnlPu0c_Z7VQxFr_uHaow$%20[rbvi[.]ucsf[.]edu]>
In ChimeraX, generally what you see is what you get in the image, so you can just try coloring, lighting and style commands (many of which you can run simply by clicking icons in the toolbar, or using the Actions menu) until you like what you see.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 20, 2023, at 4:29 AM, Mark Rosenberg via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Do you have a tutorial for ChimeraX generating publication quality surface and mesh maps with a docked model, please?
Thanks
Dr Mark F Rosenberg
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu mailto:chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Tom,
Perfect. That's what I wanted! Thank you.
Best Wishes
Mark ________________________________ From: Tom Goddard goddard@sonic.net Sent: Monday, November 20, 2023 6:18 PM To: Mark Rosenberg mark.rosenberg@manchester.ac.uk Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Tutorial
Hi Mark, Take a look at the section "Inspecting side-chain density using zones" in this ChimeraX tutorial https: //www. rbvi. ucsf. edu/chimerax/data/stanford-jul2019/tutorial2. html [rbvi. ucsf. edu] It talks about how to show the density mesh around ZjQcmQRYFpfptBannerStart This Message Is From a New External Sender You have not previously corresponded with this sender. Please exercise caution when opening links or attachments included in this message.
ZjQcmQRYFpfptBannerEnd Hi Mark,
Take a look at the section "Inspecting side-chain density using zones" in this ChimeraX tutorial
https://www.rbvi.ucsf.edu/chimerax/data/stanford-jul2019/tutorial2.html [rbvi.ucsf.edu]https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/data/stanford-jul2019/tutorial2.html__;!!PDiH4ENfjr2_Jw!FrPG7rV3SvhFgh_72Zo1tWwAFkjnLqLGH6s8H4OBCEvc8r_EXa9Q35GEGqPqRTFIa8MLDn-drLy9ybEiY0kHaO--UA$
It talks about how to show the density mesh around side chains to clearly show the quality of the map.
Tom
[density.jpg]
On Nov 20, 2023, at 9:06 AM, Mark Rosenberg via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Elanie,
I have an atomic model fitted into the map. I was looking for instructions on improving the mesh's representation with the docked atomic model.
Thank you. That was very helpful.
Kind Regards
Mark ________________________________ From: Elaine Meng <meng@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> Sent: Monday, November 20, 2023 4:21 PM To: Mark Rosenberg <mark.rosenberg@manchester.ac.ukmailto:mark.rosenberg@manchester.ac.uk> Cc: chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Tutorial
Hello Mark, If by "docked model" you mean an atomic model fitted into a map, no, there isn't a tutorial specifically about making a figure of that.
However, we have several example images along with the command scripts that were used to generate them, including at least two images that are surfaces with structures inside: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/gallery.html_... [rbvi[.]ucsf[.]edu]https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/gallery.html__;!!PDiH4ENfjr2_Jw!HhAqMVRYlcC2fo-2BxbDo0-TdAEOTcUmT5jSa9ECRyUQVfrcBwTnTI9Qu1UQj3ATeyaC-AjnlPu0c_Z7VQxFidVDdu0$%20[rbvi[.]ucsf[.]edu]>
... and numerous multi-step tutorials, including <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/tutorials.htm... [rbvi[.]ucsf[.]edu]https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/tutorials.html__;!!PDiH4ENfjr2_Jw!HhAqMVRYlcC2fo-2BxbDo0-TdAEOTcUmT5jSa9ECRyUQVfrcBwTnTI9Qu1UQj3ATeyaC-AjnlPu0c_Z7VQxFR_kSbP8$%20[rbvi[.]ucsf[.]edu]>
...intro to cryoEM maps + structures <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/data/stanford... [rbvi[.]ucsf[.]edu]https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/data/stanford-apr2022/cryoem_intro.html__;!!PDiH4ENfjr2_Jw!HhAqMVRYlcC2fo-2BxbDo0-TdAEOTcUmT5jSa9ECRyUQVfrcBwTnTI9Qu1UQj3ATeyaC-AjnlPu0c_Z7VQxFN518WzE$%20[rbvi[.]ucsf[.]edu]>
...movie-making with cryoEM data <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/data/sbgrid-ap... [rbvi[.]ucsf[.]edu]https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/cryomovie.html__;!!PDiH4ENfjr2_Jw!HhAqMVRYlcC2fo-2BxbDo0-TdAEOTcUmT5jSa9ECRyUQVfrcBwTnTI9Qu1UQj3ATeyaC-AjnlPu0c_Z7VQxFXeKFqUE$%20[rbvi[.]ucsf[.]edu]>
... ways to display/analyze ligand-protein binding sites <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/docs/user/tut... [rbvi[.]ucsf[.]edu]https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html__;!!PDiH4ENfjr2_Jw!HhAqMVRYlcC2fo-2BxbDo0-TdAEOTcUmT5jSa9ECRyUQVfrcBwTnTI9Qu1UQj3ATeyaC-AjnlPu0c_Z7VQxFr_uHaow$%20[rbvi[.]ucsf[.]edu]>
In ChimeraX, generally what you see is what you get in the image, so you can just try coloring, lighting and style commands (many of which you can run simply by clicking icons in the toolbar, or using the Actions menu) until you like what you see.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 20, 2023, at 4:29 AM, Mark Rosenberg via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
Do you have a tutorial for ChimeraX generating publication quality surface and mesh maps with a docked model, please?
Thanks
Dr Mark F Rosenberg
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edumailto:chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ [mail.cgl.ucsf.edu]https://urldefense.com/v3/__https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/__;!!PDiH4ENfjr2_Jw!FrPG7rV3SvhFgh_72Zo1tWwAFkjnLqLGH6s8H4OBCEvc8r_EXa9Q35GEGqPqRTFIa8MLDn-drLy9ybEiY0nLr6kuhQ$
participants (3)
-
Elaine Meng -
Mark Rosenberg -
Tom Goddard