Jmol Developers,
I made a mistake in 11.3.17 having to do with saving the state after
using arrays. Not a terribly big deal, but it could cause problems in
certain cases. Please wait for 11.3.18 to try the array business in the
context of "save state".
Bob
Bob Hanson wrote:
> Jmol 11.3.17 will be released soon. It includes a couple of bug fixes
> and several new Jmol math capabilities.
>
> # bug fix: problem with unescaping comma-separated point strings
> "{1,2,3}" as a point.
> # bug fix: drawn arrows scale improperly when zooming; arrow heads
> off-kilter
>
> DRAW ARROW
> ----------
> # new feature: set defaultDrawArrowScale # 0.5 initially
> # Drawn arrows now have a head size that can be set and a dimension that
> # scales with the model, so arrow head:atom size ratio remains constant
>
>
> COLOR
> -----
> Two of the color schemes introduced in 11.3.16 have been renamed since
> Angel pointed out that RasMol uses both shapely and amino.
>
> # rename byResidue_jmol --> byResidue_shapely
> # rename byResidue_rasmol --> byResidue_amino
> #
>
> CUSTOM DEFAULT COLORS
> ---------------------
> # new feature: setting Jmol,Rasmol,Shapely,Amino,Roygb,Rwb
> # color schemes makes those colors the default colors for these schemes.
>
> So if you do
>
> color "jmol=[xff0000] [xffff00] [x00ff00] [x00ffff] [x0000ff]"
>
> then when you use
>
> color atoms jmol
>
> you get your colors.
>
> New Command: PRINT
> ------------------
>
> # new feature: print command prints a variable expression
> #
> # print x
> # print x * 3
> # print x[4] + x[3]
> # print x.split(" ")[2][0]
>
> The print command prints to the console, the message queue, and the
> return value of the jmolScriptWait() JavaScript command. Basically you
> can do math and see the result. Should be helpful in debugging, but
> with the added business below, one can do something like this:
>
> x = plane({atomno=1} {atomno=2} {atomno=3})
> print {atomno=4}.distance(x)
>
>
>
> Jmol Math -- Variables as Arrays
> --------------------------------
>
> Lots new here. All simple little changes, but the combined effect is
> significant.
>
> # new feature: array variables saved as arrays
> # prior to 11.3.17, you could not do:
> #
> # x = "this is a test".split(" ")
> # y = x[3]
> #
> # because x was only saved as a string, not an array
> # now x is saved as an array, so this is no problem.
> #
>
> Jmol Math -- point() Function
> -----------------------------
> This could be considered a bug fix in that you might think that
>
> r=10;g=100;b=10;
> x = {r,g,b}
>
> would work. And now it does.
>
> # new feature Jmol math point(x,y,z) function
> #
> # point(a,b,c) or point("{x,y,z}")
> #
>
> pts = "{2,3,4}|{4,5,6}".split("|")
> pt1 = point(pts[1])
> d = point(pts[1]).distance(point(pts[2]))
>
>
> Jmol Math -- Array Element Assignments
> --------------------------------------
> You can now do this sort of thing in Jmol math:
>
> a = "2,3,4,5".split(",")
>
> a[3] = "now the 4 becomes this phrase"
> a[a[2]] = "not any more; now it's this"
> a[0] = "setting the final element"
> a[6] = "expanding the array"
> a[-1] = "setting the next-to-last element"
> print a
>
> >> 2
> >> 3
> >> not any more; now it's this
> >> setting the final element
> >> setting the next-to-last element
> >> expanding the array
>
> This works with strings as well:
>
> a = "this is a test"
> a[8] = " not" print a
>
> >> a = "this is not a test"
>
>
> Jmol Math -- plane() Function
> -----------------------------
>
> Define a plane and make measurements from it. If you give four points,
> you can designate which side you want to be the "above" the plane --
> where distances measured are positive, and which side will be "below"
> the plane -- where distances measured are negative.
>
> # new feature Jmol math plane(x,y,z,w) function
> #
> # plane(a,b,c,d) or plane("{x,y,z,w}")
> # or through three points:
> # plane({atomExprOrPoint},{atomExprOrPoint},{atomExprOrPoint})
> # or through three points with a reference point
> #
> plane({atomExprOrPoint},{atomExprOrPoint},{atomExprOrPoint},{atomExprOrPoint})
>
>
> #
> # x = plane(y[3], y[6], y[2], 3.0)
> # x = plane("{2,3,5,4}")
> # x = plane({_H}[1],{_H}[2],{_H}[3],{_C}[1])
> # print {_C}[1].distance(x)
>
> Jmol Math -- aPlane.distance({some atoms}) Function
> ---------------------------------------------------
>
> Mostly just a convenience, this measures the distance from a plane to
> the center of a set of atoms -- same as
>
> {some atoms}.xyz.distance(aPlane)
>
> The reverse:
>
> {some atoms}.distance(aPlane)
>
> measures instead the average distance of the atoms to the plane, which
> could be considerably different.
>
>
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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