Hi Elaine,

Thanks for suggestions.

I did the trick!

Best,

Lars

From: Elaine Meng <meng@cgl.ucsf.edu>
Date: Thursday, 30 November 2023 at 18:15
To: Lars Backman <lars.backman@umu.se>
Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] Missing tools in ChimeraX

Hi Lars,
We do not yet have graphical interfaces for all of the comparable settings in ChimeraX as in the Viewing Tool of Chimera.

In Chimera, the Viewing Tool combined: Camera, Side View, Rotation, Effects, and Lighting

In ChimeraX, we have similar settings for essentially all of those (and more) in commands, but only the Side View has a graphical interface currently.
<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Fsideview.html&data=05%7C01%7Clars.backman%40umu.se%7Cdcb6054dc5004dd1178c08dbf1c7ff17%7C5a4ba6f9f5314f329467398f19e69de4%7C0%7C0%7C638369613508433388%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=YNuXCB6QJGs%2BFSA4H%2B0eb7WuHBe7U5r180tMxZ6UdDo%3D&reserved=0>

Actually, the statement above is an oversimplification because ChimeraX has single-click icons in the toolbar across the top for many of the effects and lighting changes. Thus they may actually be more accessible than in Chimera once you get used to it.  Also, the Graphics tab of the toolbar has a single-click icon to show the Side View.  These icons all run commands that show up in the Log so that you can learn the commands in case you want to use them (in scripts, etc.).

See ChimeraX icon Toolbar documentation, this and links therein for the specific tabs:
<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Ftoolbar.html&data=05%7C01%7Clars.backman%40umu.se%7Cdcb6054dc5004dd1178c08dbf1c7ff17%7C5a4ba6f9f5314f329467398f19e69de4%7C0%7C0%7C638369613508433388%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=YuDCl74YXzvrmrUZjXTwzE9uW86bkb5AJtbuJ5WTMzA%3D&reserved=0>

The relevant ChimeraX commands are lighting, graphics, cofr (short for center of rotation), camera, zoom
<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Flighting.html&data=05%7C01%7Clars.backman%40umu.se%7Cdcb6054dc5004dd1178c08dbf1c7ff17%7C5a4ba6f9f5314f329467398f19e69de4%7C0%7C0%7C638369613508433388%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=VBDbjPa3CT%2BcCLn1yTGSl65Jk4%2FTfgPSCTNBaHi%2FzBw%3D&reserved=0>
<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fgraphics.html&data=05%7C01%7Clars.backman%40umu.se%7Cdcb6054dc5004dd1178c08dbf1c7ff17%7C5a4ba6f9f5314f329467398f19e69de4%7C0%7C0%7C638369613508433388%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=f%2FnRtoWT6hrhiGjGvXPs0EZFR%2BBWMMbMip4YhOfGWzw%3D&reserved=0>
<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fcofr.html&data=05%7C01%7Clars.backman%40umu.se%7Cdcb6054dc5004dd1178c08dbf1c7ff17%7C5a4ba6f9f5314f329467398f19e69de4%7C0%7C0%7C638369613508433388%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=wSgWQw6n84bVJYtY%2F8HOak%2BhE4YAitstoTIQIOs3VQY%3D&reserved=0>
<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fcamera.html&data=05%7C01%7Clars.backman%40umu.se%7Cdcb6054dc5004dd1178c08dbf1c7ff17%7C5a4ba6f9f5314f329467398f19e69de4%7C0%7C0%7C638369613508433388%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=C%2BeBSctcNSU0ijtBef2U5kLSnSGqLCxMEalqOEbEtpU%3D&reserved=0>
<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fzoom.html&data=05%7C01%7Clars.backman%40umu.se%7Cdcb6054dc5004dd1178c08dbf1c7ff17%7C5a4ba6f9f5314f329467398f19e69de4%7C0%7C0%7C638369613508433388%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ILqLKprHmdadF38Zxk06g1ABzTZTZ6pP1tIreVxCrRs%3D&reserved=0>

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 30, 2023, at 5:54 AM, Lars Backman via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hi,
> In Chimera, a tool named “Viewing” was available. It was an excellent tool to adjust appearance of the final png or jpg figure.
> I have looked for a similar tool in ChimeraX, but it seems to be absent.
> Or is there a way to create something similar?
> 
> Best regards,
> Lars Backman
>