Dear Luciano,
Below is a script that selects the frontmost atom as the molecule is
rotated by the mouse. It defines a set of 4 atoms, and whichever becomes
frontmost is selected. This script can be adapted to run any arbitrary
script triggered by one of a specified set of atoms becoming frontmost
due to rotation of the molecule with the mouse. Thus, it could be
adapted to label the frontmost atom.
The script defines a set of 4 atoms in atomlist. Every 100 milliseconds,
it runs checkOrient(), which re-determines which of the 4 atoms is
frontmost, and selects it. The selection is visible because
selectionHalos is on.
Copy the script below and paste it into the Jmol console, or paste it
into a plain text file, and drop that file into Jmol. As you rotate the
molecule with the mouse, the frontmost atom is highlighted with a yellow
halo. It does not seem to work if the molecule is spinning.
In April, 2012, we had the pleasure of a visit by Bob Hanson at our
campus (UMass, Amherst). Craig Martin's Molecular Playground (website is
currently unresponsive, but http://molecularplayground.org) was a major
topic of discussion. Karsten Theis asked Bob if, when a person rotates
the projected molecule by waving their arm, a script could be triggered
to show more detail about whatever is in front. Within one day, Bob came
up with orient.spt (below). Here is a photo commemorating this meeting:
http://proteopedia.org/w/Proteopedia:Scrapbook#Molecular_Playground_Team
-- as far as I know, this method has not yet been incorporated into
Molecular Playground modules, or any other uses.
--------------------------
// orient.spt -- tracks the orientation of four points
// This script by Robert Hanson, April, 2012 for Karsten Theis, Eric
Martz, Craig Martin.
// The frontmost of the 4 atoms specified in atomlist is selected every
0.1 sec.
// This script can be adapted to run any arbitrary script when a
specified atom
// becomes the frontmost of a specified set of atoms.
load DATA "mol"
C:/jmol-dev/bobtest/mmff94_dative.mol2
__Jmol-12_04301213583D 1 1.00000 0.00000 0
Jmol version 12.3.24_dev 2012-04-27 23:05 EXTRACT: ({0:24})
25 26 0 0 0 0 1 V2000
-8.19190 -2.59960 15.52080 N 0 0 0 0 0 0
-7.34730 -2.94810 16.47440 C 0 0 0 0 0 0
-7.02800 -2.03140 17.44970 N 0 0 0 0 0 0
-6.80300 -4.16350 16.55330 N 0 0 0 0 0 0
-7.15100 -5.04140 15.59320 C 0 0 0 0 0 0
-6.48610 -6.26490 15.62980 N 0 0 0 0 0 0
-8.03730 -4.74600 14.54960 C 0 0 0 0 0 0
-8.39880 -5.63640 13.58900 N 0 0 0 0 0 0
-9.27230 -5.22870 12.63230 C 0 0 0 0 0 0
-9.64070 -6.23510 11.58280 C 0 0 0 0 0 0
-9.79140 -3.93470 12.64140 C 0 0 0 0 0 0
-10.75920 -3.46050 11.59680 C 0 0 0 0 0 0
-9.44170 -3.03720 13.60530 N 0 0 0 0 0 0
-8.56300 -3.44580 14.55720 C 0 0 0 0 0 0
-8.61250 -1.68180 15.51700 H 0 0 0 0 0 0
-6.87870 -1.06530 17.18790 H 0 0 0 0 0 0
-6.29240 -2.39870 18.05420 H 0 0 0 0 0 0
-5.95280 -6.40360 16.48240 H 0 0 0 0 0 0
-7.05940 -7.06120 15.35990 H 0 0 0 0 0 0
-10.71720 -6.43030 11.60180 H 0 0 0 0 0 0
-9.12410 -7.18450 11.75870 H 0 0 0 0 0 0
-9.35260 -5.87520 10.59050 H 0 0 0 0 0 0
-11.04610 -2.41970 11.78010 H 0 0 0 0 0 0
-11.66930 -4.06770 11.61530 H 0 0 0 0 0 0
-10.30480 -3.51330 10.60280 H 0 0 0 0 0 0
1 15 1 0 0 0
1 14 2 0 0 0
1 2 1 0 0 0
2 4 2 0 0 0
2 3 1 0 0 0
3 17 1 0 0 0
3 16 1 0 0 0
4 5 1 0 0 0
5 7 2 0 0 0
5 6 1 0 0 0
6 19 1 0 0 0
6 18 1 0 0 0
7 14 1 0 0 0
7 8 1 0 0 0
8 9 2 0 0 0
9 11 1 0 0 0
9 10 1 0 0 0
10 22 1 0 0 0
10 21 1 0 0 0
10 20 1 0 0 0
11 13 2 0 0 0
11 12 1 0 0 0
12 25 1 0 0 0
12 24 1 0 0 0
12 23 1 0 0 0
13 14 1 0 0 0
M END
END "mol"
atomlist = ["C10","C12","N3","N6"]
function checkOrient() {
ptcenter = {*}.xyz
q = quaternion() // current rotation
asort = []
for (var i = 1; i <= atomlist.length; i++) {
var a = atomlist[i]
var pt = {atomName=a}.xyz - ptcenter
asort[i] = [a, (q%pt).z]
}
asort = asort.sort(2)
var frontAtom = (asort[0])[1]
select {atomName=frontatom}
}
selectionHalos on
# run checkOrient() every 100 milliseconds.
timeout "t1" -100 "checkOrient()"
----------------------------------------
-Eric
Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- Martz.MolviZ.Org <http://Martz.MolviZ.Org>
* Top Five 3D MolVis Tools: Top5.MolviZ.Org <http://top5.MolviZ.Org>
* FirstGlance: 3D Molecules in /Nature/: FirstGlance.Jmol.Org
<http://firstglance.jmol.Org>
* Protein 3D Structure Wiki: Proteopedia.Org <http://proteopedia.Org>
* Education: Biochem in 3D at MolviZ.Org <http://MolviZ.Org>
* Find Functional Patches in Proteins: ConSurf <http://consurf.tau.ac.il>
* Atlas of Macromolecules: Atlas.MolviZ.Org <http://atlas.MolviZ.Org>
* Interactive Molecules in Architectural Spaces:
MolecularPlayground.Org <http://molecularplayground.Org>
* Workshops: Workshops.MolviZ.Org <http://workshops.MolviZ.Org>
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