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
-------------------------------------------------------------------------
This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2005.
http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
_______________________________________________
Jmol-developers mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-developers
