13.1.x is a development branch. Wasn't thinking that we would do that.
Should we?
On Sat, Feb 23, 2013 at 8:15 AM, N David Brown <[email protected]> wrote:
> 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 <[email protected]> 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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>>
>>
>
>
> ------------------------------------------------------------------------------
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> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
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>
>
--
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
------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_feb
_______________________________________________
Jmol-users mailing list
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