Re: [Jmol-users] Slab picking: serious deficiency

[Bob H. <ha...@st...>]

11.0 will have this fixed. It's fixed in my local version right now. 
Along with  fully alignable labels, which I have almost completed.

It brings up an interesting point Miguel had mentioned some time ago -- 
what does "visible" mean? Now we have quite a bit of flexibility in this 
regard. There are currently three closely related definitions:

"visible" -- in the currently displayed model(s) and having at least one 
of wireframe, spacefill, dots, label, or secondary structure (trace, 
rockets, ribbons, cartoons, etc.). Regardless of slab.

"clickable" -- visible and not slabbed (now) and somewhat more 
restrictive in terms of secondary structure -- only some atoms are 
"clickable" there if only a cartoon is showing, for example.

"showing" -- visible, not slabbed, and within the xy limits of the window.

I'm not sure if we need to care about these at all, except perhaps with 
slab "visible" doesn't quite mean what some people might think it would 
mean.

Bob


Eric Martz wrote:

>Currently (Jmol 10.3.1), when Slab is on, clicking on the molecule reports 
>(via pickcallback) invisible atoms that are outside (e.g. in front of) the 
>visible slab. This is a serious deficiency/bug, because slabbing is an 
>important tool to simplify the view of complex molecules. Often, with slab 
>on, one wants to center or identify atoms you cannot see well with slab 
>off. But one can't.
>
>In FirstGlance in Jmol, I have had to take evasive maneuvers. I message 
>"Sorry, can't identify with slab on", and Slab is forced off when entering 
>dialogs that require clicking on atoms, such as the Contacts and Hide 
>dialogs. I block turning slab on in these dialogs (at least via the Slab 
>button).
>
>I don't know how much work it will be to fix this problem with slab, but I 
>think it is high priority because it so seriously limits the value of 
>slabbing, a tool of primary importance.
>
>-Eric
>
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