Oh, did have 2 more questions:
1) Is it possible to draw a sphere, filled or sketched like the one
on: http://accelrys.com/products/discovery-studio/pharmacophores/
pharmacophore.jpg or http://www.biomedcentral.com/content/figures/
1471-2210-6-11-7.jpg?
2) Can I add atoms/bonds via the scripting language? If not, I guess
I can create a simple input file and append it?
Cheers,
/Ola
On Jul 2, 2008, at 10:34 , Ola Spjuth wrote:
> 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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