Great stuff, thanks Bob.
Are we able to get a Maven artifact for this version? There are no 13.1.X
releases on Maven Central.
Dave
On 22 February 2013 00:27, Robert Hanson <hans...@stolaf.edu> wrote:
> I have released Jmol 13.1.13. There are several new features that may
> interest you and some bug fixes and one feature change:
>
> FEATURE CHANGE: multiple applets no longer share the same lighting space
>
> With prior versions of the Jmol applet, if you changed lighting on one
> applet on a page, the lighting changed on all applets. Now the applets are
> independent.
>
> New Features
> -------------------
> Most notably, Jmol 13.1.13 reads PyMOL session files (.PSE). There is
> still work to be done to ensure faithful rendition, but it's a start. PyMOL
> named atom sets become defined atom sets in Jmol; PyMOL "states" become
> Jmol trajectories in the case of PyMOL movies and become Jmol models in
> other cases. PyMOL movies become a new way of running animations.
>
> You can now assign color to a solvent isosurface based on the underlying
> color of the generating atom, similar to what is standard in PyMOL.
>
> Also, we now have cel shading (similar to the idea behind RCSB's "Molecule
> of the Month" visuals created by David Goodsell, but without the ray
> tracing).
>
> There are some enhanced features for loading database information
>
> ------
>
> new feature: PyMOL PSE reading
>
> new feature: animation DISPLAY {atomset}
> - applies a filter to a running animation to display only a certain
> set of atoms.
> - for example:
> load test.pse
> animation display {act_site} // defined in test.pse
> animation on
>
> new feature: animation MORPH n
> - where n is a number of frames to be inserted between trajectories
> - requires previous LOAD TRAJECTORY
> or the loading of a PyMOL PSE file having a movie (automatically a
> trajectory)
> - Jmol will do a linear morph as the animation runs.
> - for example:
> load test.pse
> animation morph 3
> animation on
> - could be used for a linear morph between just two structures:
> load trajectory "test1.pdb" "test2.pdb"
> animation morph 32 // animation will run 33 frames
> animation on
>
> new feature: frame -x.y
> - negative decimals indicate a linear morph is requested between two
> trajectory frames.
> - for example:
> load test.pse
> frame -3.5 // half way between trajectory 3 and trajectory
> 4
>
> new feature: set celShading TRUE -- produces cel shading effect
> - see http://en.wikipedia.org/wiki/Cel_shading
> - introduced by N David Brown
>
> new feature: isosurface xxxx MAP property COLOR
> -- allows inheritance of color from underlying atom (as in PyMOL)
>
> new feature: UHBD grid file reader
> new feature: DelPhi grid file reader
>
> new feature: load =xxx/ where xxx is a database code that can be set up in
> the future by a user.
> -- currently including mp MaterialsProject
> http://www.materialsproject.org/materials/%FILE/cif
> -- along with ligand, nci, nmr, pdb, pubchem
> -- see JmolConstants.databases for the full list.
> -- note that nci can take an additional tag such as /names after the
> name, and pubchem can take one before it:
>
> load =mp/1
> load =nci/caffeine
> load =pubchem/caffeine
> load =pubchem/cid/2345
> print(load('=nci/caffeine/names'))
>
> Bug fixes
> ========
>
> bug fix: set picking IDENT when picking is already ident can cancel a
> pending measurement
> bug fix: applet does not refresh when mouse exits with pending measurement
>
> bug fix: labels within fog should be hidden
> bug fix: load CENTROID does not always work -- wrong implicit
> normalization flag (was -1 instead of 1)
>
> bug fix: property_xxx does not work (since 10/3/12, 13.1.7)
>
> bug fix: The "show history" command is supposed to clear out the "show
> history" command
> itself, but only if it is a top-level command (from the console),
> but it does more than that if it is part of script("show
> history").
> Probably true with all recent versions of Jmol.
>
> bug fix: isosurface binary file reading (MRC, CCP4, O, binary PMESH, etc.)
> broken
>
> bug fix: JavaScript: zoomTo [seconds > 0]... and restore
> rotation|orientation [name] [seconds > 0] not waiting
>
>
>
>
>
>
>
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> 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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