Hola, Angel :-)
Thanks a lot for your tips, this was exactly what I needed. Will post
my visualizations here later so that you may see the results.
Cheers,
/Ola
On Jul 1, 2008, at 19:52 , Angel Herraez wrote:
> 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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