transparency command doesn't work on nucleotide representations

[Elaine Meng]

Unlike the color command, the transparency command has no "target f" and even if all targets are specified with "All" the nucleotide representations remain opaque. Reported by user:

From: Yan ZHANG 张艳 via ChimeraX-users <chimerax-users@…>
Subject: [chimerax-users] How to change transparency of ladder mode of nucleic acids
Date: March 14, 2024 at 1:27:33 AM PDT
I am writing to seek assistance regarding how to change transparency of ladder mode of nucleic acids in ChimeraX. Despite trying the command 'trans #1 60 all', I have been unable to achieve the desired effect.

Could you please suggest an alternative solution or provide guidance on how to accomplish this task?

From: Elaine Meng via ChimeraX-users <chimerax-users@…>
Subject: [chimerax-users] Re: How to change transparency of ladder mode of nucleic acids
Date: March 14, 2024 at 5:35:22 PM PDT
To: Yan ZHANG 张艳 <zhangyan30@…>

Dear Zhang Yan,
I can see this problem -- unfortunately, it is a current limitation of the "transparency" command. It applies to the cartoon (ribbons) but not the nucleotide representations: ladder, stubs, ellipsoids, etc.

I will make a ticket for this problem in our bug database and include your email so that you will be notified if the problem is fixed.

There is a workaround but it is not convenient. The "color" command has a "target f" option that does apply to the nucleotide representation of each residue. So you can use "color" with its "transparency" option instead of the "transparency" command, but you have to give a color in the command. So if your ladders have several different colors you would have to know which residues are which colors, and then use several different color commands.

Here is an example of making the ladder transparent tan:

color #1 tan transparency 60 target f

Or for a specific residue, residue number 5 in chain A, with yellow ladder:

color #1/A:5 yellow transparency 60 target f

Info about "color" command:
<​https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple>

I hope this helps, and sorry for the inconvenience!
Sincerely,
Elaine

[Greg Couch]

Fixed. Noticed that there is no support for 2d labels, nor undo support.