A visualization of protein or nucleic acid secondary structure. Applying this to other molecules will not show anything.
In nucleic acids, the base cylinders obtain their color from the atom to which the cylinder is drawn, which is 'N1' for purines (resn: 'A', 'G', 'DA', 'DG') and
'N3' for pyrimidines (resn: 'C', 'U', 'DC', 'DT').
The different nucleobases can therefore be distinguished as by setting the colors
of each of these atoms. The backbone color is set from the 'P' atoms ('O5' for the 5' terminus).
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Example
$3Dmol.download("pdb:4ZD3",viewer,{},function(){
viewer.setBackgroundColor(0xffffffff);
viewer.setViewStyle({style:"outline"});
viewer.setStyle({},{cartoon:{}});
viewer.render();
});Members
arrows :boolean
whether to add arrows showing beta-sheet
directionality; does not apply to trace or ribbon
- boolean
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color :ColorSpec
strand color, may specify as 'spectrum' which will apply reversed gradient based on residue number
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colorfunc :function
Allows the user to provide a function for setting the colorschemes.
- function
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colorscheme :ColorschemeSpec
colorscheme to use on atoms; overrides color
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hidden :boolean
do not show
- boolean
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opacity :number
set opacity from 0-1; transparency is set per-chain
with a warning outputted in the event of ambiguity
- number
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ribbon :boolean
whether to use constant strand width, disregarding
secondary structure; use thickness to adjust radius
- boolean
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style :string
style of cartoon rendering (trace, oval, rectangle (default), parabola, edged)
- string
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thickness :number
cartoon strand thickness, default is 0.4
- number
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tubes :boolean
whether to display alpha helices as simple cylinders;
does not apply to trace
- boolean
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width :number
cartoon strand width, default is secondary
structure-dependent; does not apply to trace or ribbon
- number
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