Re: [Jmol-users] Optimal "bring to front" command

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

very good idea. Miguel and Frieda and I were just talking about something like 
this.

Eric Martz wrote:

> I believe a new "bring to front" command would be extremely useful. By 
> this I mean a single command that would bring any atom or set of atoms 
> "to the front" in the following steps:
> 
> 1. The molecule would be rotated so the selected set is in front.
> 
> 2. The selected set would move SMOOTHLY to the center over a specified 
> number of seconds (without any change in zoom, please).
> 
> 3. Optionally, the proposed command could include a zoom-up value, or 
> else it could be followed by a separate move command for zooming purposes.
> 
> The point of this command is that steps 1 and 2 could be performed 
> automatically for any arbitrary atom or atom set, notably sets not 
> "known in advance". An example of use: clicking on a residue in a 
> sequence listing would bring that residue to the front, center it, and 
> optionally zoom in.
> 
> This functionality differs from the (laborious) situation where the 
> moiety to be brought in front and centered is known in advance, and the 
> desired final orientation is determined empirically and entered in a 
> "moveto" command.
> 
> ---------------------------------------
> THOUGHTS ON IMPLEMENTATION
> 
> If doing the rotation and centering (and zooming) all at once is tricky 
> to implement, I would be perfectly happy if these operations were done 
> in separate consecutive stages.
> 
> 1. ROTATION. The desired rotation can be determined from the vector 
> defined by two centers of mass, one for the seleted set, and the other 
> for atoms within a modest distance of the selected set. This vector 
> would then be rotated so it is perpendicular to the screen, with the 
> selected set in front. (See Notes below*).
> 
> 2. CENTERING. It is desirable that the selected set can be centered in a 
> smooth slide, such as generated by a move command, so the viewer can 
> grasp what is happening.
> 
> SUGGESTED COMMAND FORMAT
> 
> Someone can probably think of a better name for the command, but it 
> could be called "bringtofront".
> 
> bringtofront [atomset] [seconds-for-rotation] [distance] 
> [seconds-to-center] [zoom]
> 
> where
> 
> [distance] means the distance in Angstroms from the center of the 
> [atomset] used for determining the center of mass for the "rear" of the 
> rotation vector.
> 
> [zoom] need not be part of this command, but could be.
> 
> It would be nice if all parameters were optional (but all parameters to 
> the left of any specified must be specified. Thus
> 
> bringtofront
> 
> (with no parameters) would operate on the currently selected set, using 
> 2 seconds for both times, no change in zoom, and a default distance to 
> be determined by some experimentation.
> 
> bringtofront selected 3.0 10.0 3.0 50
> 
> would rotate to position the selected atoms in front (over 3 seconds, 
> using a distance of 10.0 Angstroms to determine the rear center of 
> mass), then slide the selected atoms to center over 3 seconds, then 
> incease the zoom by 50%.
> 
> COMMENTS WELCOME!
> 
> -Eric
> 
> [*Notes: If one used the center of mass of the entire molecule for the 
> second point, this would only work well for spherical molecules. Using a 
> local neighborhood of atoms for the second point will work, I believe, 
> for prolate or oblate shaped molecules.
> 
> This algorithm has limitations that are acceptable to me.
> 
> Limitation A. It will not work for an atom in the inside of one of the 
> globules of a dumbbell-shaped molecule. That would require slabbing as 
> well, and I am not proposing that we automate slabbing here.
> 
> Limitation B. It will not make a buried atom in a spacefilled rendering 
> visible. The user would need to use a backbone trace to see a buried atom.
> 
> Limitation C. The selected atoms should be contiguous. Selecting atoms 
> on opposite sides of the molecule would not make sense.
> 
> End of Notes.]
> 
> 
> 
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--

Robert M. Hanson, ha...@st..., 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
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"Imagination is more important than knowledge." - Albert Einstein