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

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.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__;!!PDiH4ENfjr2_Jw!HhAqMVRYlcC2fo-2BxbDo0-TdAEOTcUmT5jSa9ECRyUQVfrcBwTnTI9Qu1UQj3ATeyaC-AjnlPu0c_Z7VQxFidVDdu0$ [rbvi[.]ucsf[.]edu]>

... and numerous multi-step tutorials, including
<https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/tutorials.html__;!!PDiH4ENfjr2_Jw!HhAqMVRYlcC2fo-2BxbDo0-TdAEOTcUmT5jSa9ECRyUQVfrcBwTnTI9Qu1UQj3ATeyaC-AjnlPu0c_Z7VQxFR_kSbP8$ [rbvi[.]ucsf[.]edu]>

...intro to cryoEM maps + structures
<https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/data/stanford-apr2022/cryoem_intro.html__;!!PDiH4ENfjr2_Jw!HhAqMVRYlcC2fo-2BxbDo0-TdAEOTcUmT5jSa9ECRyUQVfrcBwTnTI9Qu1UQj3ATeyaC-AjnlPu0c_Z7VQxFN518WzE$ [rbvi[.]ucsf[.]edu]>

...movie-making with cryoEM data
<https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/cryomovie.html__;!!PDiH4ENfjr2_Jw!HhAqMVRYlcC2fo-2BxbDo0-TdAEOTcUmT5jSa9ECRyUQVfrcBwTnTI9Qu1UQj3ATeyaC-AjnlPu0c_Z7VQxFXeKFqUE$ [rbvi[.]ucsf[.]edu]>

... ways to display/analyze ligand-protein binding sites
<https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html__;!!PDiH4ENfjr2_Jw!HhAqMVRYlcC2fo-2BxbDo0-TdAEOTcUmT5jSa9ECRyUQVfrcBwTnTI9Qu1UQj3ATeyaC-AjnlPu0c_Z7VQxFr_uHaow$ [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

_______________________________________________
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/