[Jmol-users] Jmol 16.3.35/16.3.36

[Robert H. <ha...@st...>]

see
https://sourceforge.net/projects/jmol/files/Jmol/Version%2016.3/Jmol%2016.3.35

Quite a variety of mostly specialized bugs here. A few changes for
JSpecView in association with the IUPAC FAIRSpec project metadata extractor
implementation.

Thank you to all who have contributed bug reports. GO, OPEN SOURCE!

Bob

Jmol.___JmolVersion="16.3.35" // (legacy) also 16.3.36 (swingJS)

feature change: Switching to new nmrdb prediction API for 1H and 13C
predicted spectra
  -- uses a POST of JSON
  -- see https://nmr-prediction.service.zakodium.com/v1/documentation/
  -- see https://chemapps.stolaf.edu/jmol/jsmol/testEPFL2.htm
  -- see https://chemapps.stolaf.edu/jmol/jsmol/testEPFL2-13C.htm
  -- see https://chemapps.stolaf.edu/jmol/jsmol/jsv_predict2.htm

new feature: COLOR ISOSURFACE VERTICES ({...}) green
  -- bit set of vertices to color
  -- generally not advised, but part of PyMOL session loading

bug fix: PyMOL surface translucency not read
  -- adds support for partially translucent PyMOL surfaces

bug fix: WRITE ISOSURFACE or WRITE xxx.jdxl  creating unnecessarily large
files
  -- specifically for PyMOL files, size drops by up to 90% (500K to 50K)

bug fix: WRITE MESH not working
  -- should create a "vertex-only" (not linear marching cube) JVXL file
  -- these are much larger than the linear marching cube JVXL files

bug fix: coloring a read JVXL-based isosurface does not re-save new color
in write JVXL

bug fix: PDB files will not display unit cell with standard load
  -- broken in 16.2.24

bug fix: MOPAC v.23 not loading
  -- modified header not recognized

bug fix (legacy only): JME interface not accepting MOL files with a blank
first line

bug fix (legacy only): JSpecView interface fails for empty <peakInfo>
element

bug fix: various JSpecView upgrades
  -- expanded nmrML reading
  -- better JDX header processing for IUPAC FAIRSpec
  -- better connection between Jmol and JSpecView for reading
     files with both structure and spectra (JDX, nmrML)

bug fix: protein structure starting at residue 1 but not first in listing
not created

bug fix: SMILES generator for allenes broken in 16.3.10




-- 
Robert M. Hanson
Professor of Chemistry, Emeritus
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

*We stand on the homelands of the Wahpekute Band of the Dakota Nation. We
honor with gratitude the people who have stewarded the land throughout the
generations and their ongoing contributions to this region. We acknowledge
the ongoing injustices that we have committed against the Dakota Nation,
and we wish to interrupt this legacy, beginning with acts of healing and
honest storytelling about this place.*