[Jmol-developers] Jmol navigation success

[Bob H. <ha...@st...>]

Jmol developers:

We will soon be introducing quite a radically new capability to Jmol: 
scripted and user-directed navigation. The idea is to be able to follow 
a path THROUGH a model, not just hold it at arm's length and rotate it. 
Charles Xie and I are quite excited about this. To date we have:

set navigationMode TRUE/FALSE
set perspectiveStyle 11/10 # (10 disallows navigation)
set hideNavigationPointer
set showNavigationPointerAlways
set picking navigation # mouse clicking sets the navigation center position
set visualField x.xx # number of angstroms across at observer position 
(5.0 by default)
set cameraDepth x.xx # number of screens from front of model to camera 
(3.0 by default)

The above commands allow for 100% backward compatibility with Jmol 
10.2/11.0 because you can specify to use the Jmol 10 perspective 
algorithms (default) or the new version. The 10.2 is kept because zoom 
settings are quite different in navigation mode. (No more need for huge 
zoom values when you can just zip on up to an atom and poke it in the 
electron.)

These next commands don't exactly speak for themselves, but I suspect 
you can get the idea of what we are after from them, and with a bit of 
experimentation you will find them quite useful. Obviously these will 
need some tweaking.

navigation nSec depth p # a depth value, like slab, in percent (0 rear, 
100 front)
navigation nSec rotate X degrees
navigation nSec rotate Y degrees
navigation nSec rotate Z degrees
navigation nSec translate x.xx y.yy  # percentages; 0 0 center
navigation nSec translate X x.xx # relative percent
navigation nSec translate Y y.yy # relative percent
navigation nSec translate {x y z}
navigation nSec translate $object # could be a draw object
navigation nSec translate (atom selection) #average of values
navigation nSec center {x y z}
navigation nSec center $object
navigation nSec center (atom selection)
navigation nSec path $object indexStart indexEnd
navigation nSec path (atom expr) {x y z} (atomexpr) (atomexpr) {x y z} 
etc...
navigation nSec path {x y z theta} {x y z theta}{x y z theta}{x y z 
theta}...

In addition, once you have invoked

set navigationMode

the user has keyboard access (although I've had some problem with this 
on the applet, which I don't understand). It SHOULD behave as follows:

UP/DOWN arrows -- go forward, back off
LEFT/RIGHT arrows -- look left, look right
ALT UP/DOWN arrows -- look up, look down
SHIFT LEFT/RIGHT arrows -- shift navigation point left, right
SHIFT UP/DOWN arrows -- shift navigation point up, down

slabbing in this mode is automatically set to be at the position of the 
observer.
I have written up a discussion of the Jmol perspective/navigation model. 
You can find it at 
http://www.stolaf.edu/academics/chemapps/jmol/docs/misc/navigation.pdf

Happy holidays.

Bob