Happy New Year to all Jmol users!
Nico will release 11.1.5 soon (whenever you can, Nico).
This version of Jmol contains some very significant additional features:
Navigation Mode
-------------------------------
With this release you can now navigate through a model. There are some
tricks; see the documentation for help on this. Be sure you select
documentation for version 11.1, not 11.0. Commands include:
set navigationMode
set cameraDepth x.xx
set hideNavigationPoint
set navigationMode TRUE/FALSE
set navigationSlab [depth from navigation point; positive toward user]
set navigationSpeed [5]
set navigationPeriodic # for crystals, creates the effect of an infinite
array in all directions
set perspectiveModel 11/10 # (10 disallows navigation)
set picking navigation
set modelRadius x.xx
set showNavigationPointAlways
set visualRange x.xx
navigation nSec center {x y z}
navigation nSec center $object
navigation nSec center (atom selection)
navigation nSec depth p # a depth value, like slab, in percent (0 rear,
100 front)
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}...
navigation nSec rotate X degrees
navigation nSec rotate Y degrees
navigation nSec rotate Z degrees
navigation nSec trace (atom expression)
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
an interesting test is
load 1crn.pdb;cartoons on;color cartoons group
set sheetSmoothing 0;set traceAlpha
set navigationMode
navigate trace (*)
Hold on to your hat -- it's a bumpy ride! The arrow keys work the
navigation as well.
Periodic Boundary Conditions
-------------------------------
In navigation mode if you load a crystallographic model with one or more
unit cells (I recommmend at least {5 5 5} and then set the unit cell to
be in the middle, with, perhaps,
load graphite.cif 1 {10 10 10};axes off;unitcell off
unitcell {4 4 4};
and then
set navigationPeriodic
you can create the the illusion of an infinite surface. Basically, when
the navigation center leaves the unit cell, it reenters from the
opposite side, always creating the illusion of more atoms than are
actually in the model.
Internal Slabbing
-------------------------------
I first thought about this last summer but couldn't figure out how to do
it. But now, with the perspective model better in mind, I realized it
was almost trivial to implement. The idea is slab/depth planes that
rotate with the model -- that are defined based on model coordinates,
not screen coordinates. So you can now, for example:
slab plane x = 3
slab reference {0 0 0}
slab on
and the slabbing will rotate with you as you rotate the model with the
mouse. This to me is very exciting. I think the old slab style will be
of minimal interest once you try this. The reference point is necessary,
because it is no longer obvious which side to display without that --
the side with the reference point is displayed.
You can get just a slice of a model using both depth and slab:
slab plane x = 3; slab depth x = -1;
slab reference {0 0 0}
slab on
Try this with
isosurface sasurface
and you will have some fun --- oh, and then turn navigation mode on!
Probably a few bugs. This is brand new.
Other goodies
---------------
set allowEmbeddedScripts OFF # turns off allowing embedded scripts,
mostly for testing
set zShade # shadows increase with distance from the user; experimental
Bob
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