Add lighting user interface to avoid sooty ambient shadows

[Tom Goddard]

Krishna Reddy notes in this tweet that it is useful to increase the number of shadow directions to avoid soot

​https://twitter.com/firewhenreddy/status/1572583216665759746

"Tired of seeing your beautiful @UCSFChimeraX structure look like a 50s coal miner? Default settings don't use enough shadows (for rendering speed): use "lighting multishadow 512" to crank it up before capturing your figure. You're welcome, no need to offer me co-first authorship."

[Tom Goddard]

Elaine:

I'll try to add something to the docs somewhere about trying more light directions as an "image tip". I have said a few times in responses (or maybe it's in an example image description) to try "light gentle" instead of "light soft" to decrease the sootiness. One issue is that the icon just does "light soft" so most people just click the icon and then accept the result rather than trying to use other command options.

Tom:

You are right. Probably most people only know lighting modes through the toolbar icons. Maybe worth adding two more lighting icons Fast and Lovely that would use the current mode but adjust shadow directions and texture sizes for speed vs quality. Or I could add just one toolbar button that brings up a lighting tool that shows more lighting parameters with sliders so you can try different values.

Tom also tweeted another common lighting tweek:

Cruel and true. The default 64 shadow directions is fast but sooty. Another ambient shadow trick "lighting msDepth 0.005 multishadow 256" darkens small crevices compared to the default value of 0.01. Phage T4 capsid PDB 5vf3.

Elaine:

(without consulting docs because I'm in the middle of working on something else)... is that "lighting gentle"? Even if you don't have an icon for some useful group of settings, an intermediate approach is to make a lighting preset by that name.

Tom:

No, gentle uses larger depth bias rather than smaller. The docs don't describe the lighting preset settings, might be useful to document those. More presets are easy to add but they will help very few people because there is no user interface other than commands to discover those additional lighting presets. I guess the Presets menu could have a Lighting rollover that lists all the lighting presets.

Elaine:

Sorry, delete the nonsensical "by that name" part from previous message. Brain is destroyed today.
The trick with presets is to make a select few that work well in a wide range of situations, much easier said than done. Similar to our smart initial display.

[Elaine Meng]

I tried to put short "English" explanations of the presets. I guess you meant the exact values of all the parameters in each. I'll do that soon, maybe link "details..." after each short explanation to a separate section at the end of the lighting manpage that lists them in detail.

[Elaine Meng]

To facilitate use in scripts, i think it would still help to have a preset or shorter alias for each icon's corresponding command if you do decide to add more lighting icons.

[Elaine Meng]

I updated the "lighting" command help page to include detailed parameter lists for each preset.  I also added the tip to increase the number of multishadows to counteract sootiness (same place in "soft" description where I'd put my previous tip to try "gentle" instead).  

I doubt many people are bothering to read the lighting command help page for these tips anyway, but maybe it will reach a few!. These changes are currently only on preview but should show up on the main website after the next successful daily build.  Preview:
<https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/commands/lighting.html#preset">

Elaine

[pett]

Also, from Anne-Frances Miller <afmill3r2@…>:

[Chimera's] Lighting/effects/side view GUI that allows easy optimization of figure reflectivity, special effects, all in one place and does not require users to remember what Cartesian coordinates they gave their first light. It is so much faster and delivers much better results than ChimeraX.

[Tom Goddard]

I agree that a lighting gui that offers controls like the number of multishadow directions would make it much easier for users to discover these obscure parameters that allow fine tuning the image appearance. That said, I think most users are able to make beautiful publication images using default lighting modes. The trouble is mostly user working with small molecules with ribbons and sticks and trying to use soft lighting where it is not suitable. So I would not say the lighting gui is a high priority -- I think it will be rarely used because the defaults are working well for the majority of users.