Some thoughts:
-- What is happening is that zooming has placed an atom behind the camera.
It must be removed. the camera position has reached the If you use *set
slab 100; set slabByAtom *you can prevent the bond from being slabbed
itself; same with atoms.
-- Starting with Jmol 11.0 zooming is linear. The camera by default is 3
"molecular diameters" (including a margin for spacefill) in front of the
model "reference plane" (*show cameraDepth*). The model itself sits 1/2
molecular diameter further from the camera than the reference plane. "100%
zoom" is the largest setting for which no part of the model, when rotated,
passes in front of this reference plane. Bonds for which either associated
atom lies behind the camera are clipped. So it is guaranteed that *zoom 600*
will still present the model with no clipping. Above that, in some
orientations, you will start to see slabbing.
-- There is no "maxZoom" option in Jmol. If there were, it would be this
cameraDepth * 200. You could set that yourself by turning sync on, setting
a SyncCallback, checking the zoom each time the callback is called
(whenever the model is reoriented) and using that to force the zoom down to
cameraDepth * 200 if it goes over that.
-- See http://chemapps.stolaf.edu/jmol/docs/misc/navigation.pdf for the
gory details.
Bob
On Thu, Mar 12, 2015 at 10:05 AM, Rolf Huehne <[email protected]>
wrote:
> Hi all,
>
> if a model is shown in ball and stick representation, some bonds
> suddenly disappear completely at some zoom level although parts of them
> should still be visible.
>
> Q: I am wondering what the criteria are for a bond to disappear?
>
> Q: Is there any way to stop zooming before the first bond disappears to
> avoid a misleading representation?
>
> Regards,
> Rolf
>
> --
>
> Rolf Huehne
> Postdoc
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department 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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conversation now. http://goparallel.sourceforge.net/
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