Re: [Jmol-users] Label a bond?

[Angel H. <ang...@ua...>]

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