Bob:
I am seeing “unrecognized file format” errors in this release for both PubChem
and RCSB.
> On Mar 21, 2016, at 2:38 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
> This update takes care of a few minor bugs and also introduces several
> powerful features in relation to polyhedra, unit cells, and SMILES.
>
> Jmol.___JmolVersion="14.4.4_2016.03.21"
> released
>
> new feature: moveto axis [a1-c4]
> -- extends moveto axis a|b|c to all for corners 1|2|3|4
> where 1 is upper left, 2 is upper right, 3 is lower right, and 4 is lower
> left
> -- for example, MOVETO AXIS a3
> -- defaults: a==a1, b==b1, c==c4
>
> new feature: axes OFFSET x.x
> -- applies offset of x.x in fractional coordinates in each axis direction
> -- AXES OFFSET -0.1 same as AXES CENTER {-0.1 -0.1 -0.1/1}
>
> new feature: expanded unitcell() function
> -- adds additional types: "A", "B", "C", "I", "F"
> -- default is the lattice type of the model's space group
> -- not just cubic; "BCC" is converted to "I"
> -- for example:
>
> load =ams/silicon 15 packed // Cmca
> draw id "uc" diameter 0.1 unitcell mesh nofill color black
> unitcell @{unitcell("primitive")}
> color unitcell red
> unitcell 0.1
> axes unitcell
> axes on
>
> new feature: expanded UNITCELL command to include PRIMITIVE option for any
> space group
>
> new feature: show smiles/NCI aka show smiles/CACTVS aka show
> smiles/canonical
>
> -- generates nonaromatic SMILES and sends that to NCI for canonicalization
>
> bug fix: SMILES matcher not allowing azulene to be aromatic
>
> bug fix: OpenSMILES matcher not allowing non-chemist Hueckel 4+2
> interpretation
>
> bug fix: SMILES generator not adding "-" for biphenyl Ar-Ar bond
>
> bug fix: set picking invertSTEREO does not work on open-ring systems
>
> bug fix: SMARTS [R] matching all atoms
>
> bug fix: dashed lines not visible in measurements, unit cells, and axes
>
> bug fix: axes 0.01 produces thick 20-pixel-wide lines
> -- solution was to drop that to 0.001 for this effect
>
> bug fix: Polyhedra with verticies that are also centers of polyhedra for
> atoms that were visible
> but are no longer visible do not update screen positions properly
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr <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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> Accelerate data analysis in your applications with
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Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu
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