I'd like a newer artifact for the embedded Jmol instances being used in my
own Maven project, since I would like cel shading to be available.
I tried running jmol-sonatype.xml myself in eclipse after successfully
completing a build.xml. It complained that
build/dists/pom.xml.templatecouldn't be found.
I then tried copying that template file to the specified location and
copying build/*.jar into the same directory too. The build proceeds happily
for a while, then prints:
[artifact:mvn] [ERROR] BUILD ERROR
[artifact:mvn] [INFO]
------------------------------------------------------------------------
[artifact:mvn] [INFO]
D:\projects\svn\Jmol\build\dist-maven\jmol-null-SNAPSHOT.jar not
found.
Any suggestions how to build an artifact?
Cheers,
Dave
On 23 February 2013 20:49, Robert Hanson <hans...@stolaf.edu> wrote:
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 <hubd...@gmail.com> 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 <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
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> 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
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> 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
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> 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
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