Roni,
Yeah, that's a bit cryptic.
Slab. First, realize that there are two kinds of slab now. You can define
any plane to be a slab plane. (by the ax +by +cz = d method, or by defining
three atoms, or a number of other ways). So that, for example, you can whack
off a piece of the protein and then still rotate it about with the mouse and
that part will always be gone. This, I believe, is a unique feature of Jmol.
Or you can slab by percent of depth, as in Chime and Rasmol and many other
programs. So for that you want to know the size of the bounding box. Not a
problem. A little scripting will get that for you.
point1 = getProperty("boundboxInfo.corner0")
point2 = getProperty("boundboxInfo.corner1")
Now the z distance is just
dz = point2.z - point1.z
and you can slab in percent using that, say, at 12 angstroms forward from
the rear edge:
slab @{(12/dz*100)%0};slab on
note that we have to round the value (12/dz*100) using "%0" because slab
only take integer arguments.
note also that the boundbox corners are based on the "reset" orientation
(molecular coordinates) and do not change with orientation.
Bob Hanson
On Wed, Mar 18, 2009 at 9:33 AM, Roni Gordon <[email protected]>wrote:
> Hello,
>
> Just wondering if there's an easy way to change slab (or
> equivalently, depth) based on an absolute amount (e.g. A or nm)
> rather than a relative percentage of boundbox (which I what I think
> it's based upon based on the docs). Alternatively, if this is not
> possible, is there a simple method of calculating and determining
> what the approriate % would be?
>
> Along the same lines, I recently noticed that v11.8 has a "translate
> Z" that also can operate on absolute amounts -- and this effectively
> adjust the zoom level. However, the docs state that this "Adjusts
> the zoom setting such that the specified number of angstroms or
> nanometers are added/removed from the field of view at the midpoint
> depth of the model, as defined by the dimension from which zoom is
> referenced ". Does that imply that the model is already translated
> to half of the boundbox "depth" based on the specified zoom
> dimension? Is this value easily obtained? I'm also a bit confused
> on how modelRadius fits into this mix.
>
> Thanks in advance for any clarifications,
>
> Roni
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
easily build your RIAs with Flex Builder, the Eclipse(TM)based development
software that enables intelligent coding and step-through debugging.
Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
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