transparency command does not work on nucleotides (target f)

[Elaine Meng]

Although I had not yet documented target f for the transparency command, the usage given in the Log includes it, so I'm calling this a bug. Details in this e-mail exchange:

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From: Siyu Chen <siyuchen2021@…>
Subject: [chimerax-users] Set transparency on DNA stubs
Date: October 16, 2020 at 12:43:42 PM PDT
To: chimerax-users@…

Dear chimerax developers,
I am writing to ask about an issue regarding to the transparency of DNA bases.

I set the double strand DNA as stubs and colored cyan, and I wanted to set it as transparent (trans 70 tar c). However, it looks like only the DNA backbones become transparent, and the bases are still bright and solid. I even tried to throw in all possible targets into the 'trans' command (acrsbpfl) and got the same looking images. I am just wondering if this is because of the style or color that makes the bases look solid? Also, do you have other suggestions to get around this issue?

Thanks in advance for your time and help!
Best,
Siyu Chen

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From: Elaine Meng <meng@…>
Subject: Re: [chimerax-users] Set transparency on DNA stubs
Date: October 16, 2020 at 1:32:38 PM PDT
To: Siyu Chen <siyuchen2021@…>
Cc: chimerax-users@…
Reply-To: ChimeraX Users Help <chimerax-users@…>

Dear Siyu Chen,
I believe this is a bug, or at least a limitation of the "transparency" command. The "f" target is supposed to include nucleotide representations. I will make a bug-report ticket for this -- thanks for letting us know. It may not have been implemented yet, since I see that the "transparency" manual page does not list it currently:
<​http://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html>

What works currently is the "color" command with target f, and you can include transparency in the color command. It is not as convenient if there are multiple colors, since you would need a separate color command for each color, instead of a single transparency command. However, in your case, it sounds like all the stubs are already the same color and you would be able to use a single command, for example:

color nucleic cyan trans 50 targ f

<​http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple>

I hope this helps,
Elaine

[Greg Couch]

I think it that it only looks like it doesn't work due to the single level of transparency. The command "color nucleic cyan trans 50 targ f" does make the slab transparent, but you can only tell if there is non-transparent stuff behind it.

[Elaine Meng]

Is there some technical reason this can't be fixed?

[Greg Couch]

ChimeraX (and Chimera) only do a single level of transparency. Multiple levels would require rewriting the graphics code to support multiple passes and/or more complicated shaders. I think everyone agrees that it would be nice to have more levels of transparency, even just 2, 3, or 4 levels would be great. But the code complexity has held us back.

[Elaine Meng]

This bug report is not about multiple layer transparency.  It is whether you can make nucleotide representations transparent (which would function under the current state of single-layer transparency just like the transparency of all the other representations that can be made transparent now).

[pett]

Yes, as per the description in the ticket, this is about the *transparency* command with target 'f' not changing nucleotide depictions, not the *color* command.

[Greg Couch]

So a transparency command example is:

transparency #1 50 target f

[Elaine Meng]

duplicate of #14769