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Re: [Jmol-users] Jmol 12.3.15 released Philip Bays Sun Feb 12 19:00:26 2012

Bob:

In your examples link blow, the jspecview applet does not load for me in either 
Safari or Firefox.   The error message indicates that the applet "cannot be 
found".

Pbil

On Feb 12, 2012, at 6:59 PM, Robert Hanson wrote:

> Thanks, Nico, for releasing 12.3.15. It's got one very big new feature and 
> several others. As well as a few bug fixes.
> 
> Primarily, JSpecView is now merged into Jmol. This means that the 
> distribution of Jmol includes the JSpecView applet (jspecview.jar). and the 
> JSpecView application is embedded in the Jmol application. You  can view 
> spectra and click on spectral peaks to display vibrations or mass spec 
> fragments or to highlight atoms in NMR spectra. And, conversely, you can 
> display vibrations or fragment models or click on atoms to see the 
> corresponding spectrum. You can see it in operation at 
> http://chemapps.stolaf.edu/jmol/docs/examples-12/jspecview/test1.html . 
> 
> This is all made possible by two new records Robert Lancashire has introduced 
> into JCAMP-DX files. These add model data and peak assignments. 
> 
> #version=12.3.15
> 
> # bug fix: SLAB unit cell not showing all lines
> # bug fix: CRYSTAL reader needs to change to MOLECULAR when X(ANGSTROMS) 
> found (fullerene slab)
> # bug fix: Popup Menu item hbond calculate should not require PDB
> 
> # new feature: context menu Spectra submenu
> 
>   (used for displaying spectral information from JDX files)
> 
> # new feature: JSpecView integration into Jmol application  and SYNC 
> communication with applet
> #  -- if model/peak-enhanced JDX file is read, clicking on an atom or 
> switching
> #     to an IR vibration or MS fragment displays the appropriately 
> highlighted spectrum/fragment
> # new feature: JCAMP-DX file reading
> #  -- reading of ##$MODELS and ##$PEAK_LINKS (see 
> http://chemapps.stolaf.edu/jmol/docs/examples-12/jspecview)
> 
> # new feature: model ID "..."
> #  -- can be file-specific using "filename#..."
> #  -- used for correlating non-Jmol synced applets
> # new feature: sync ~ 'Select: xxx'
> #  -- xxx can include file="xxx" model="xxx" atoms="xxx" select="xxx" 
> script="xxx"
> #  -- file and model combined as model ID "file#model"
> #  -- will automatically load the file if the given file#model ID is not found
> #  -- atoms = list of atom numbers separated by commas: 1,2,3 --> @1 or @2 or 
> @3
> #  -- select is any valid selection such as THR or 1-30 
> #  -- automatically adds "visible &" to atoms or select 
> #  -- requires sync ON
> 
> # new feature: NFF neutral file format reader 
> (http://paulbourke.net/dataformats/nff/nff1.html)
> #              for electron microscopy data exported from IMOD
> 
> # new feature: when picking struts or delete bond or measure, distance shows 
> as per usual measurement
> 
> 
> 
> 
> -- 
> 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
> ------------------------------------------------------------------------------
> Virtualization & Cloud Management Using Capacity Planning
> Cloud computing makes use of virtualization - but cloud computing 
> also focuses on allowing computing to be delivered as a service.
> http://www.accelacomm.com/jaw/sfnl/114/51521223/_______________________________________________
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J. Philip Bays
Emeritus Professor of Chemistry
Department of Chemistry and Physics
Saint Mary's College
Notre Dame, IN 46556
[EMAIL PROTECTED]





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