cartoon preset undisplays too much

[Greg Couch]

For 2adw, selecting the cartoon preset appears to hide NCY and N2C residues, so the protein polymer is disconnected if cartoon is turned off. But the DSN and MVA residues are shown.

Also, with so few atoms (1652), would prefer a different initial display:
cartoon; nuc tube; style protein stick
But not sure how feasible that is. Perhaps relax the limit on the number of chains if there aren't many atoms.

[Elaine Meng]

Cartoon preset always gives disconnected residues if cartoon is then turned off, because atomic detail is just around the binding sites.  Also, I think it’s a losing proposition to try to make the initial display rules more and more elaborate to get an ideal initial view of every structure.  We just want it work for a large proportion, with a reasonably small set of rules that people can remember and understand.  After that, try to make changing aspects of the display as easy as possible because different people will want different things, and even the same person will want different things depending on the task at hand.

[Greg Couch]

I see. Wouldn't it be more useful and less surprising if the mainchain atoms were hidden using the normal ribbon mechanism? That way they would appear when the ribbon is turned off? I am always surprised when nothing is shown.

[pett]

Agree with what Elaine said vis a vis fine tuning of presets. I eventually want to offer user control over the various preset "levels" and I don't want that interface to have thousands of tuneables, so simpler is better.

Treating this as a request to leave backbone displayed (but hidden) in cartoon preset.

--Eric

[Elaine Meng]

It’s debatable whether any change should be made.  I personally prefer the backbone atoms not to be shown by the cartoon preset because often one wants to show only the atoms around the binding pocket.  In the current behavior, if you hide the cartoon, you are left with exactly that, and not mysterious stringy backbone atoms that will confuse people because their sidechains aren’t also shown.

[pett]

Closing this since the requested behavior is problematic in other usage scenarios, and is pretty specific to the usage scenario described. For instance, if you use the cartoon preset and then use the stick preset, everything is fine. To get the problem you have to use the cartoon preset and then the ~cartoon command. Basically there is no "fix" that is clearly an improvement.

[Greg Couch]

I'm still confused by this. Choosing to display the cartoon representation using the icon, gives the desired behavior for NCY and N2C. But the cartoon preset is doing something extra that messes things up.

And there is no "undo" for the preset.

[Elaine Meng]

No idea what structure you are looking at.  Might be something weird with autochaining and nonstandard residues.

[pett]

As per the original description: 2adw

[Elaine Meng]

Seems fairly specific to this unusual structure and relates to "ligand" classification. This has a bunch of DNA with some short peptides crosslinked to each other, and each crosslinked peptide molecule has some atoms that are "ligand" and some atoms that are not. Only the ligand atoms get displayed, whereas all of the peptides are classified as protein and thus have cartoons. To clarify, get rid of extraneous stuff:

open 2adw
delete nucleic
delete solvent
delete H
(use cartoon preset)
select ligand
select protein

At first I thought maybe the ligand shouldn't be classified as ligand, but then again, there are several things that are covalently attached to a protein that we do want as ligand (retinal in rhodopsin etc.). I guess these peptides have too many atoms to be entirely classified as ligand. The cartoon preset itself looks fine. It is only if somebody chooses cartoon preset and then un-cartoon that is confusing (and why did you choose cartoon preset if you didn't want cartoons?). I think it is not confusing when you have a regular-sized protein with or without ligands. In this weirder case, a person could choose sticks preset or "show" to see all atoms, or "show mainchain" to display backbone.