Re: [Jmol-users] Jmol 14.14.1

2017-04-19 Thread Robert Hanson 
hmm. something is missing there. I had to delete that and will upload again.

On Wed, Apr 19, 2017 at 11:28 PM, Robert Hanson  wrote:

> Jmol.___JmolVersion="14.14.1" // released 4/19/17
>
> new feature: CALCULATE CHIRALITY {atom set}
>   -- starts with basic CIP Rule 1-2 determination of R/S and E/Z.
>   -- continues with Rules 3-5, which require full-molecule analysis.
>   -- work in progress:
>  -- Rules 1 and 2 complete
>  -- Rule 3 (E/Z) implemented
>  -- Rule 4 partially implemented
> -- simple linear sequences of R/S ok
>  -- Rule 5 not implemented
>   -- caveates
>  -- no pseudochirality
>  -- not cyclitols
>  -- does not distinguish rings, so inserts "Z" into ring bonds
>  -- only validated on
>
>   -- optionally limited to the given atom set (or the currently selected
> atoms by default)
>
> new feature: set jmolInJSpecView
>   -- allows Jmol window to NOT be embedded in JSpecView when JSpecView is
> opened in Jmol
>   -- default TRUE
>
> new feature: WRITE ISOSURFACE "t.pmesh"; WRITE ISOSURFACE "t.pmb"
>   -- creates ASCII (.pmesh) or binary (.pmb) file (a Jmol-specific file
> format)
>   -- relatively compact format
>   -- can speed up loading of meshes and contours
>   -- for filled surfaces, use .jvxl instead
>   -- read back into Jmol using ISOSURFACE "t.pmesh"/"t.pmb"
>   -- note that binary files are NOT RECOMMENDED for JSmol because some
> platforms cannot read them locally
>   -- example:
>
>   load $methane
>   isosurface plane {0 0 0 1} map vdw contours 20
>   write ISOSURFACE contour.pmb
>   isosurface contour.pmb
>
>
> bug fix: mesh capper producing gaps
> bug fix: CIP chirality fixed for rule ordering; validated for IUPAC Rules
> 1, 2, and 3 (though still some questions about Rule 3)
> bug fix: print getProperty("cifinfo") without file name fails
>
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> 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
>
>


-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol 14.14.1

2017-04-19 Thread Robert Hanson 
link for this release: * Download Jmol-14.14.1-binary.zip (65.0 MB)
 *

On Wed, Apr 19, 2017 at 11:28 PM, Robert Hanson  wrote:

> Jmol.___JmolVersion="14.14.1" // released 4/19/17
>
> new feature: CALCULATE CHIRALITY {atom set}
>   -- starts with basic CIP Rule 1-2 determination of R/S and E/Z.
>   -- continues with Rules 3-5, which require full-molecule analysis.
>   -- work in progress:
>  -- Rules 1 and 2 complete
>  -- Rule 3 (E/Z) implemented
>  -- Rule 4 partially implemented
> -- simple linear sequences of R/S ok
>  -- Rule 5 not implemented
>   -- caveates
>  -- no pseudochirality
>  -- not cyclitols
>  -- does not distinguish rings, so inserts "Z" into ring bonds
>  -- only validated on
>
>   -- optionally limited to the given atom set (or the currently selected
> atoms by default)
>
> new feature: set jmolInJSpecView
>   -- allows Jmol window to NOT be embedded in JSpecView when JSpecView is
> opened in Jmol
>   -- default TRUE
>
> new feature: WRITE ISOSURFACE "t.pmesh"; WRITE ISOSURFACE "t.pmb"
>   -- creates ASCII (.pmesh) or binary (.pmb) file (a Jmol-specific file
> format)
>   -- relatively compact format
>   -- can speed up loading of meshes and contours
>   -- for filled surfaces, use .jvxl instead
>   -- read back into Jmol using ISOSURFACE "t.pmesh"/"t.pmb"
>   -- note that binary files are NOT RECOMMENDED for JSmol because some
> platforms cannot read them locally
>   -- example:
>
>   load $methane
>   isosurface plane {0 0 0 1} map vdw contours 20
>   write ISOSURFACE contour.pmb
>   isosurface contour.pmb
>
>
> bug fix: mesh capper producing gaps
> bug fix: CIP chirality fixed for rule ordering; validated for IUPAC Rules
> 1, 2, and 3 (though still some questions about Rule 3)
> bug fix: print getProperty("cifinfo") without file name fails
>
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> 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
>
>


-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] Jmol 14.14.1

2017-04-19 Thread Robert Hanson 
Jmol.___JmolVersion="14.14.1" // released 4/19/17

new feature: CALCULATE CHIRALITY {atom set}
  -- starts with basic CIP Rule 1-2 determination of R/S and E/Z.
  -- continues with Rules 3-5, which require full-molecule analysis.
  -- work in progress:
 -- Rules 1 and 2 complete
 -- Rule 3 (E/Z) implemented
 -- Rule 4 partially implemented
-- simple linear sequences of R/S ok
 -- Rule 5 not implemented
  -- caveates
 -- no pseudochirality
 -- not cyclitols
 -- does not distinguish rings, so inserts "Z" into ring bonds
 -- only validated on

  -- optionally limited to the given atom set (or the currently selected
atoms by default)

new feature: set jmolInJSpecView
  -- allows Jmol window to NOT be embedded in JSpecView when JSpecView is
opened in Jmol
  -- default TRUE

new feature: WRITE ISOSURFACE "t.pmesh"; WRITE ISOSURFACE "t.pmb"
  -- creates ASCII (.pmesh) or binary (.pmb) file (a Jmol-specific file
format)
  -- relatively compact format
  -- can speed up loading of meshes and contours
  -- for filled surfaces, use .jvxl instead
  -- read back into Jmol using ISOSURFACE "t.pmesh"/"t.pmb"
  -- note that binary files are NOT RECOMMENDED for JSmol because some
platforms cannot read them locally
  -- example:

  load $methane
  isosurface plane {0 0 0 1} map vdw contours 20
  write ISOSURFACE contour.pmb
  isosurface contour.pmb


bug fix: mesh capper producing gaps
bug fix: CIP chirality fixed for rule ordering; validated for IUPAC Rules
1, 2, and 3 (though still some questions about Rule 3)
bug fix: print getProperty("cifinfo") without file name fails




-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users