Here's another new option "set zshadepower" that could be fun to experiment
with. Notice the intense fog
http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm?load%20quartz-action.png;set%20slabcleanly;set%20zshadepower%203
On Tue, Jan 19, 2010 at 6:45 AM, Robert Hanson <[email protected]> wrote:
> A wee bit better perhaps, with this option I'm experimenting with:
>
>
> http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm?load%20quartz-action.png;set%20slabcleanly
>
>
> On Tue, Jan 19, 2010 at 6:42 AM, Robert Hanson <[email protected]> wrote:
>
>> Mouse wheel -- right, Rolf. That is a change. That was toned down because
>> it was just way too difficult to control (in my opinion), but we can revert
>> that if you think what we have now is just too slow. Let's talk about that.
>> Since I don't have a mouse wheel, I'm probably not the one to ask, but the
>> problem, as I recall, is that other actions are sometimes sent to Jmol as a
>> mouse-wheel action, and that "super zooming" that was set up for that was
>> way too much.
>>
>>
>> Major thanks to Eric for helping me get electron density going. I'm not
>> sure why exactly, but Eric doesn't have the latest Jmol development
>> (unreleased) version up there. Maybe I didn't get that uploaded properly.
>> This version:
>>
>>
>> http://www.umass.edu/molvis/tests/jmol_edm_test4/?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolAppletSigned.jar
>>
>> which should be in
>> http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip, does not
>> have any of the problems Eric refers to there. Also, as far as I can tell,
>> slab has been and still is working just fine.
>>
>> slab 60
>> slab on
>>
>> Again, using JVXL files (which are now XML) greatly improves the download
>> performance -- obviously you are not going to show map files that are 65Mb
>> on the web!
>>
>> Eric, another thing you might try is the FRONTONLY option for the
>> isosurface. Warren Delano told me that that's better for mesh
>>
>> In addition, you might want to experiment with
>>
>> set navigationMode on
>>
>> with controls by mouse or keyboard arrows, and possibly
>>
>> navigation on
>>
>> (though that takes some practice, because the keyboard arrows are
>> ACCELERATORS, like banking an aircraft. (In an aircraft, the controls are
>> used to establish the bank - i.e. accelerate -- then centered during the
>> bank to maintain it.) The spacebar key stops the navigation until another
>> key is pressed.
>>
>> This is an alternative to slab and instead of looking at the molecule
>> through a microscope with slabbing to "fake" being there, this setting
>> actually brings you into the molecule and lets you traverse it. No slabbing
>> necessary.
>>
>> An example of this is given in the example
>> http://chemapps.stolaf.edu/jmol/docs/examples-11/quartz-action.png, which
>> will "play" in Jmol with
>>
>>
>> http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm?load%20quartz-action.png
>>
>> which also demonstrates periodic boundary condition navigation through a
>> crystal and also a very new zshade mode that allows you to adjust the power
>> of the shading so that it is nonlinear. It was an effect we needed for the
>> upcoming Epcot Center exhibit, "Touch a Molecule".
>>
>> Bob
>>
>>
>> On Tue, Jan 19, 2010 at 4:50 AM, Rolf Huehne <[email protected]>wrote:
>>
>>> On 01/18/2010 09:03 PM, Eric Martz wrote:
>>> > I have made a little demonstration of visualization electron density
>>> maps in Jmol, showing off some of Bob's recent innovations.
>>> > http://www.umass.edu/molvis/tests/jmol_edm_test4/
>>> >
>>> > This new capability of Jmol is just fantastic!
>>> >
>>> I agree!
>>>
>>> While checking out the demonstration I noticed a change in mouse
>>> behaviour between version 11.9.20_dev and 11.6.8 (which we are currently
>>> using within Jena3D (http://jena3d.fli-leibniz.de):
>>>
>>> If I zoom the example structure '3hyd' after providing a 'reset' command
>>> using the Jmol script console with the mouse wheel it takes about 14
>>> full strokes until the atoms in the middle fill out the whole applet.
>>> If I do the same with version 11.6.8 only about 3 full strokes are
>>> necessary. (http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=3hyd)
>>>
>>> To exclude any differences in the initial Jmol settings between Eric's
>>> site and Jena3D I also tested it with the new version within Jena3D with
>>> the same result.
>>> (
>>> http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=3hyd&APPLET=signed&JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolAppletSigned0.jar
>>> )
>>>
>>> Was this change in mouse behaviour intentional or accidental?
>>> Do others also observe a similar change on other systems?
>>> (Test system: openSUSE 11.2 x86_64, Java 1.6.0_17, Firefox 3.5.6)
>>>
>>> If it was intentional I think it is too fine-grained as a default. You
>>> might say that there is additionally the new zoom function at the right
>>> edge of the applet and the zoom with Shift-mouse_move, both zooming much
>>> less fine-grained. And it might be a good idea to have some differences
>>> here to provide different levels of control. But even with this idea I
>>> still think it is currently too fine-grained.
>>> What do you think about this?
>>>
>>> Regards,
>>> Rolf
>>>
>>>
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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
>>
>
>
>
> --
> 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
>
--
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
------------------------------------------------------------------------------
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
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