Port topography command from Chimera to ChimeraX

[Tom Goddard]

The topography command might be useful for visualization atomic force microscopy data. I've been talking to Yuzhen Feng about AFM data of viruses that he wants to align to PDB models and this may be a nice way to look at that data.

[Tom Goddard]

Done.

The topography command is mostly the same as in Chimera with the following changes. The colorMap keyword is now palette. There is also a range keyword for the range of values to use with the palette. The default palette is now none. The height option still gives the full range of heights but the surface has height zero at the image plane whereas in Chimera it had the minimum height at the image plane. This handles signed data better. There is a color option that specifies the surface color (if palette not used), default (180,180,180,255).

[Elaine Meng]

I added docs, currently previewable here
https://www.cgl.ucsf.edu/home/meng/chimerax/docs/user/commands/topography.html#palette-options

However, I suspect there is a bug in this command.  No matter which plane of the data I am actually showing, it appears to use the data from some other specific plane that stays the same.  I can tell because the zero appears to be offset from the plane I am showing, and the topography looks the same even though the plane I am viewing looks totally different, and it stays in the same place no matter which plane I show before using the command.

[Tom Goddard]

Could you give me an example where it is not displaying the right plane. I tested many cases and it always showed the correct plane and correct data for me. For example,

open 1080 from emdb
volume #1 plane z,50
topo #1
volume #1 plane z,70
topo #1

volume #1 region all
volume #1 plane x,60
topo #1

[Elaine Meng]

I must have been doing something wrong last week, since today I cannot reproduce the problem even with what I believe is exactly the same data and same commands... which is a  surprise since I spent quite a bit of time testing it.  Apologies for the "user error" -- I will close the ticket.

[Tom Goddard]

I bet there is some bug, but it takes some magic step to get it to happen.  If someone sees it and reports it I can fix it then.

[Tom Goddard]

Docs look fine.  I kind of liked the clean style of the Chimera version of the topography documentation where each option had a description.

	https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/topography.html

[Elaine Meng]

I tend to use that kind of documentation with options in blockquotes when there are a high number of options.  This command was borderline, with the decision to not do it that way because the palette options are already documented separately and it was somewhat awkward to have both a "palette-options" link and a "options-other-than-palette-options" link in the usage.  There is a hybrid approach to both list them at the top and in an options section, but then referring to a different page for palette options is confusing.  There is so much documentation of palette options that I don't want to duplicate that whole section in each other page that uses them: mlp, topo, and potentially others.