From: Robert H. <ha...@st...> - 2013-02-23 20:49:24
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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 <hu...@gm...> 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 <ha...@st...> 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 >> Jmo...@li... >> 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 > Jmo...@li... > 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 |