Hi Ola
(in Spanish: Hola, Ola :-)
> I'd like to draw a line between two atoms and label the line. How can
> I achieve this in jmol?
The command (dates back to RasMol and Chime) is "monitor"
synonyms: measure, measurement
Oh, no! You want a custom label, and that will only be good for no
label or a distance label.
One solution is to use "draw"
example: if your atoms are number 3 and 5,
draw myLine (atomno=3) (atomno=5)
set echo myEcho $myLine
echo Ola
You can use instead any other way to identify the atoms; put
parentheses around.
You can specify line width, line color, and label color:
draw myLine width 0.15 color yellow (atomno=3) (atomno=5)
set echo myEcho $myLine
echo Ola
color echo yellow
> Can I use 'select' and 'label' together, like
> 'select bond X; label "myLabel"'?
I don't think you can select bonds, but you can select atoms:
set echo myEcho {atomno=3 or atomno=5}
echo myLabel
or
define bondX atomno=3 or atomno=5
set echo myEcho {bondX}
echo myLabel
> Also, is it possible to add a
> custom label to an angle between 3 atoms?
Not using measure, I think. But you can use either echo (3D-
positioned) or draw (a point in 3D space):
draw myAngle (O2) (C1) (C3) #this will draw a solid triangle
set echo myEcho {O2 or C3} # no commas inside braces, must use OR
echo Ola's angle
or, line instead of triangle:
draw myAngle1 (O2) (C1)
draw myAngle2 (C1) (C3)
set echo myEcho {O2 or C3}
echo Ola's angle
or even
draw myAngle1 (O2) (C1)
draw myAngle2 (C1) (C3)
draw myLabel "Ola's angle" {O2 or C3}
Or, if you prefer this look:
measurement (O2) (C1) (C3)
set measurementLabels off
set echo myEcho {O2 or C3}
echo Ola's angle
color echo white
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