On 29 Nov 2009 at 9:54, Andy Lu wrote:
> In Jmol, the default setting for selectionHalos on is all of the atoms, or
> you can select more
> specific types of protein residues, ex. Arg, His, Aromatic, etc.
The setting is to show halos for all SELECTED atoms. You define what you want
selected.
> But I want to be able to select halo on only for a certain number of residues
> of my choice read
> from a string array.
As I said, you can select any subset you want, and the selectionHalos will be
displayed for
those. I still don't get where is your problem.
And later
On 29 Nov 2009 at 10:51, Andy Lu wrote:
> One more question, I try to draw an arrow or line between 2 residues, any
> idea how I would go
> about?
> I tried, the following, but it's only showing up as a dot.
>
> viewer.evalString("draw ARROW (" +proteinIDGlobal1[1] +"," +
> proteinIDGlobal1[4]+");");
I cannot help you with evalString, but I guess it will work the same as a plain
script:
Please check out the DRAW syntax
you need to give two atoms or coordinates to get a line (or arrow) drawn. If
you give one,
you get a dot.
Probably you must remove the comma and the parentheses.
e.g.
draw arrow {1 1 0} {1 3 0}
maybe:
viewer.evalString("draw ARROW " +proteinIDGlobal1[1] +" " +
proteinIDGlobal1[4]+";");
> Also if I try to draw an arrow between 2 residues, where on the residue does
> the line connects
> them? Alpha carbon?
The line connects whatever point or atom you used to specify it.
If your proteinIDGlobal1[1] variable refers to the resiude, that will be the
geometric center of
the resiude atoms. You can choose e.g. the alpha carbon by doing
viewer.evalString("draw ARROW " +proteinIDGlobal1[1] +" and alpha " +
proteinIDGlobal1[4]+" and alpha;");
or "and *.CA" instead of "and alpha" if it is a pdb file.
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