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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