Re: [Jmol-users] Jmol 14.17.1

[fziegler]

Bob:

Spiro works fine. Thanks. I realize you are a fan of Gibbs. Gibbs lab has been 
demolished. Neither of the 2 new residential colleges were named in his honor 
but he is being “honored” by a walkway!

http://news.yale.edu/2017/02/23/celebrating-history-gibbs-lab-and-future-science-yale

Fred


Professor Frederick E. Ziegler, Emeritus
Sterling Chemistry Laboratory 
225 Prospect Street
Yale University 
P.O. Box 208107   
New Haven, Connecticut 06520-8107   
E-mail: frederick.zieg...@yale.edu  
Telephone: (203) 432-3959   
   






> On May 27, 2017, at 1:13 PM, Robert Hanson  wrote:
> 
> Jmol-14.17.1-binary.zip (69.8 MB) 
> 
> Jmol.___JmolVersion="14.17.1"  // 2017.05.27
> 
> new feature: atom property x.cipRule 
>  -- CIP sequence rule deciding this center  
>  -- one of 1a, 1b, 2, 3, 4a, 4b, 4c, 5, or blank
> 
> bug fix: polyhedra broken in Jmol 14.10.0
> 
> bug fix: finalizing CIP algorithm
>  -- adding spiro chirality from P-93.5.3
>  -- completing root path for auxiliary descriptors 
> 
> bug fix: JSmol: JSME/JSmol 2D->3D fails when one H of a CH2 is explicitly 
> wedge and the other H is implicit (not shown at all). (JSmolJME.js)
> 
> code:
> 
> /**
>  * A fully validated relatively efficient implementation of Cahn-Ingold-Prelog
>  * rules for assigning R/S, M/P, and E/Z stereochemical descriptors. Based on
>  * IUPAC Blue Book rules of 2013.
>  * https://iupac.org/projects/project-details/?project_nr=2001-043-1-800 
> 
>  * 
>  * Features include:
>  * 
>  *  - deeply validated 
>  *  
>  *  - implemented in Java (Jmol) and JavaScript (JSmol)
>  *  
>  *  - only two Java classes; roughly 1000 lines
>  *  
>  *  - efficient, one-pass process for each center using a single finite 
> digraph for all auxiliary descriptors
>  *  
>  *  - exhaustive processing of all 8 sequence rules (1a, 1b, 2, 3, 4a, 4b, 
> 4c, 5)
>  *  
>  *  - includes R/S, r/s, M/P (axial, not planar), E/Z
>  *  
>  *  - covers any-length odd and even cumulenes
>  *  
>  *  - uses Jmol conformational SMARTS to detect atropisomers and helicenes 
>  *  
>  *  - covers chiral phosphorus and sulfur, including trigonal pyramidal and 
> tetrahedral
>  *  
>  *  - properly treats complex combinations of R/S, M/P, and seqCis/seqTrans 
> centers (Rule 4b)
>  * 
>  *  - properly treats neutral-species resonance structures using fractional 
> atomic mass and a modified Rule 1b
>  *  
>  *  - implements CIP spiro rule (BB P-93.5.3.1)
>  *  
>  *  - detects small rings (fewer than 8 members) and removes E/Z 
> specifications for such
>  * 
>  *  - detects chiral bridgehead nitrogens
>  *  
>  *  - reports atom descriptor along with the rule that ultimately decided it
>  * 
>  * Primary 236-compound Chapter-9 validation set (AY-236) provided by Andres
>  * Yerin, ACD/Labs (Moscow).
>  * 
>  * Mikko Vainio also supplied a 64-compound testing suite (MV-64), which is
>  * available on SourceForge in the Jmol-datafiles directory.
>  * (https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/cip 
> ).
>  * 
>  * Additional test structures provided by John Mayfield.
>  * 
>  * Additional thanks to the IUPAC Blue Book Revision project, specifically
>  * Karl-Heinz Hellwich for alerting me to the errata page for the 2013 IUPAC
>  * specs (http://www.chem.qmul.ac.uk/iupac/bibliog/BBerrors.html 
> ), Gerry Moss
>  * for discussions, Andres Yerin for discussion and digraph checking.
>  * 
>  * Many thanks to the members of the BlueObelisk-Discuss group, particularly
>  * Mikko Vainio, John Mayfield (aka John May), Wolf Ihlenfeldt, and Egon 
> Willighagen, for
>  * encouragement, examples, serious skepticism, and extremely helpful advice.
>  * 
> 
> 
> -- 
> 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
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Re: [Jmol-users] ivxl

[fziegler]

Bob:

Thanks for your rapid response. Will try jvxl and 14.15.2

Fred


> On Apr 29, 2017, at 4:11 PM, Robert Hanson  wrote:
> 
> Fred, 
> 
> I had no problems with this in just-released 14.15.2:
> 
> $ isosurface ch3cl-density.cub.gz map ch3cl-esp.cub.gz
> $ write isosurface t.jvxl
> 
> reading isosurface data from c:/jmol-dev/bobtest/ch3cl-density.cub.gz
> reading isosurface data from c:/jmol-dev/bobtest/ch3cl-esp.cub.gz
> isosurface1 created  with cutoff=0.02 min=0.0 max=1.35334; isosurface count: 1
> isosurface full data range -0.007748252 to 10.191908 with color scheme 
> spanning -0.007748252 to 10.191908
> 1 id:isosurface1; model:0.0; vertices:1982; polygons:3960; visible:true; 
> dataRange:[-0.007748252, 10.191908, -0.007748252, 10.191908]; 
> title:isosurface ch3cl-density.cub.gz map ch3cl-esp.cub.gz;
> 
>isModelConnected="false" 
>   cutoff="0.02" 
>   isCutoffAbsolute="false" 
>   pointsPerAngstrom="5.6691847" 
>   nBytesData="6620" 
>   isXLowToHigh="true" 
>   nSurfaceInts="612" 
>   nBytesUncompressedEdgeData="1981" 
>   nBytesUncompressedColorData="3964" 
>   precisionColor="true" 
>   colorMapped="true" 
>   color="[x5020a0]" 
>   translucency="0.0" 
>   colorScheme="roygb" 
>   rendering="fill noMesh noDots notFrontOnly frontlit" 
>   dataMinimum="-0.007748252" 
>   dataMaximum="10.191908" 
>   valueMappedToRed="-0.007748252" 
>   valueMappedToBlue="10.191908" 
>   note="progressive JVXL+ -- X values read from low(0) to high(49)" 
>   xyzMin="{-1.5917101 -1.3869982 -2.2582495}" 
>   xyzMax="{1.5907205 1.6996462 1.9228424}" 
>   approximateCompressionRatio="not calculated" 
>   jmolVersion="Jmol 14.15.2  2017-04-29 14:09">
> 
> 
> OK XJVXL 7884 c:/jmol-dev/bobtest/t.jvxl
> $ zap
> $ isosurface t.jvxl
> reading isosurface data from c:/jmol-dev/bobtest/t.jvxl
> isosurface1 created  with cutoff=0.02001; isosurface count: 1
> isosurface full data range -0.007748252 to 10.191908 with color scheme 
> spanning -0.007748252 to 10.191908
> 1 id:isosurface1; model:0.0; vertices:1982; polygons:3960; visible:true; 
> dataRange:[-0.007748252, 10.191908, -0.007748252, 10.191908]; 
> title:isosurface t.jvxl;
> 
> $ 
> 
> 
>  
> You released 14.15.1, we installed it (not online), along with esomeprazole 
> (chiral S). Configuration shows up but no double bonds when installed under 
> EZ or EZ and RS groups.  We are working on it. Any thoughts?
> 
> Some aspects of chirality were broken in 14.15.1. I think. See most recent at 
> https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.15/Jmol%2014.15.2/
>  
> 
> 
>  
>  Fred
> 
> PS: This message precedes “follow-up”.
> 
> --
> Check out the vibrant tech community on one of the world's most
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> 
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> 
> 
> 
> 
> 
> -- 
> 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
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[Jmol-users] ivxl

[fziegler]

Bob:

I didn’t see my response to jvxl issues posted. Here it is again.

Here is what i do with 14.15.1 using console in Jmol.jar (It works fine in 
14.2.9)

$ isosurface filename_den.cub map filename_esp.cub (four to five blue lines 
appear.)
$ write isosurface filename.jvxl
S (no blue text appears. Nothing written.)

 My associate guru, Misha, has had the same experience.

Something else.

Misha has programmed RSEZcombo.html with 14.14.1, works great. 
http://ursula.chem.yale.edu/~chem220/chem220js/STUDYAIDS/isomers/RSEZcombo/RSEZcombo.html
 


You released 14.15.1, we installed it (not online), along with esomeprazole 
(chiral S). Configuration shows up but no double bonds when installed under EZ 
or EZ and RS groups.  We are working on it. Any thoughts?  Fred

PS: This message precedes “follow-up”.--
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[Jmol-users] Follow up ?

[fziegler]

Bob:

It is my understanding that you have implemented the CIP sub-rule “Z precedes 
E”. For (4R, 2Z, 5E)-4-methylhepta-2,5-diene, R, E and Z are displayed using 
the console. But we cannot display R on

http://ursula.chem.yale.edu/~chem220/chem220js/STUDYAIDS/isomers/RSEZcombo/RSEZcombo.html

E and Z do appear. We use j2s and JSmol.min.js on the website. Is there another 
file required?  Confused in New Haven. Fred
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Re: [Jmol-users] Jmol 14.15.1

[fziegler]

Bob and Bruce:

Bruce: Happy to see writing jvxl files working for you. No luck here with 
14.15.1 using Gaussian cube files. Any thoughts. Fred

 
> On Apr 28, 2017, at 2:46 PM, Bruce Tattershall 
>  wrote:
> 
> Bob
>  
> The version you published yesterday works fine for finding chirality in my 
> organo PS cage compounds
> (e.g. with 67 atoms), both in JSmol and in Jmol_S.
>  
> The problem with writing mo  jvxl files is also fixed for me.
>  
> Contour plots on a plane .pmesh files do come back with the same colour 
> scheme they had before saving,
> but if one changes this to colour scheme bw, I have not found any way to 
> switch back to the saved colours,
> other than reloading the file.  The original isosurface plane was coloured 
> with colour scheme bwr, but if
> I reapply this, the contours come out all white.   Any ideas?
>  
> Thanks
>Bruce
>  
> From: Robert Hanson [mailto:hans...@stolaf.edu] 
> Sent: 28 April 2017 19:11
> To: jmol-users@lists.sourceforge.net
> Subject: Re: [Jmol-users] Jmol 14.15.1
>  
> OK, that version is broken for CIP chirality determination in JavaScript. Ran 
> into an odd Java->JavaScript problem that requires recompilation. Simple 
> structures will work, but more advanced issues will cause atoms to not 
> display a chirality designation with label %[chirality]. JavaScript only; 
> Java is fine.
> 
> 
> 
> Bob
>  
> On Thu, Apr 27, 2017 at 8:41 PM, Robert Hanson  > wrote:
> Jmol.___JmolVersion="14.15.1" // 4/28/17
> 
> bug fix: values not saved in state for cartoonBlockHeight, cartoonBlocks, and 
> cartoonSteps
> bug fix: write MO broken
> bug fix: set cartoonBlockHeight (for DSSR nucleic acid rendering) fails
> 
> new feature: x.split(true)
>  -- does a white-space token split of the string value of x
> 
> new feature: MOL/SDF reader reads M  ISO  lines for isotopes
> new feature: CIP chirality adds P, S, As, Se, Sb, Te, Bi, Po trigonal 
> pyramidal and tetrahedral
> new feature: CIP chirality adds imine and diazine E/Z chirality
> 
> bug fix: CIP chirality broken for carbonyl groups
> bug fix: CIP chirality E/Z should not be indicated for rings of size < 8
> 
> code: CIPChirality.java 779 lines Rules 1-5 validated on 145 compounds 
>   - see 
> https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/cip/ 
> 
> code: CIP optimizations
> 
> 
> 
> -- 
> 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

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[Jmol-users] R/S-E/Z

[fziegler]

Bob:

We have expanded an RS html to include EZ 
[http://ursula.chem.yale.edu/~chem220/chem220js/STUDYAIDS/isomers/RSEZ/RSEZexercises.html
 
].

There are several questions.

1) Can the RS tags be separated from the EZ tags? Just to simplify the display.

2) Is there a reason both sp2 carbons in double bonds are tagged? Is one E/Z 
tag over the double bond possible?

3) Example (2Z,5E)-4-methyl-2,5-heptadiene displays EZ but not the 
R-configuration. Exploring this example on the Jmol console, the 
R-configuration appears.
All other examples at the link work fine.


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[Jmol-users] E/Z and isosurfaces

[fziegler]

Bob:

Thanks for including E/Z functionality in the R/S module. Will add it to

http://ursula.chem.yale.edu/~chem220/chem220js/STUDYAIDS/isomers/RS/RSexercises.html
 


On the subject of isosurfaces, jmol 14.6.4 thru 14.14.1 have not been able to 
write jvxl files from Gaussian generated cube files, i.e.,

isosurface filename_den.cub map filename_esp.cub
write isosurface filename.jvxl 
(no file written!)

 Is there any effort afoot to fix this problem?

Jmol 14.0.13 and 14.2.9 still do the job.

Thanks, Fred Ziegler--
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Re: [Jmol-users] I there a problem with isosurfaces in jmol-14.6.4_2016.10.02

[fziegler]

Prof. Hanson:

Nice job with the RS module. I assume at this stage more complex sequence rules 
are not handled, e.g., seqcis precedes seqtrans [(2Z, 5E)-2, 5-heptadien-3-ol] 
and (+)-inositol. Tried them but no RS designation. As to another matter, I 
contacted you in October about the inability of Jmol.jar in Jmol 14.6.4 to 
write jvxl files. I notice that this is still a problem in Jmol-14.12.1. Any 
thoughts? Thanks, Fred Ziegler
> On Oct 30, 2016, at 6:24 PM, Robert Hanson  wrote:
> 
> Sorry for the delay - I don't know of any other reports relating to the 
> console. Certainly nothing new there in a long time -- since the addition of 
> a font scale button. Anyone else having this issue?  --- Jmol.jar 
> specifically.
> ​
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[Jmol-users] Is there a problem with isosurfaces in jmol-14.6.4_2016.10.02?

[fziegler]

I have been using jmol-14.2.9_2014.11.23 to make electrostatic potential maps. 
[See: http://ursula.chem.yale.edu/~chem220/chem220js/StudyAids.html#ESP] 


I use Gaussian to generate cube files. I open jmol.jar>console and type:

$ isosurface cutoff 0.02 filename_den.cub map filename_esp.cub
$ write isosurface filename.jvxl

All is well.

I downloaded jmol-14.6.4_2016.10.02

The console does not appear to work properly. If the line $ isosurface cutoff 
0.02 filename_den.cub map filename_esp.cub is added, blue text appears with 
cutoff 0.0.

Typing $ write isosurface filename.jvxl gives only a return of the prompt $. No 
jvxl file is written. Multiple entries do not work. Jmol.jar must be closed and 
reopened to make an entry. Still no positive result.

I have taken jmol.jar from jmol-14.2.9_2014.11.23 and put it in 
jmol-14.6.4_2016.10.02. It works but places the file in the former Jmol folder. 
I can redirect the jvxl file with write isosurface /Users/…/filename.jvxl.

But this not an advantage. 

Is there a problem with jmol.jar in mol-14.6.4_2016.10.02?

Thanks for your help, Fred Ziegler--
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[Jmol-users] I there a problem with isosurfaces in jmol-14.6.4_2016.10.02

[fziegler]

I have been using jmol-14.2.9_2014.11.23 to make electrostatic potential maps. 
[See: http://ursula.chem.yale.edu/~chem220/chem220js/StudyAids.html#ESP]

I use Gaussian to generate cube files. I open jmol.jar>console and type:

$ isosurface cutoff 0.02 filename_den.cub map filename_esp.cub
$ write isosurface filename.jvxl

All is well.

I downloaded jmol-14.6.4_2016.10.02

The console does not appear to work properly. If the line $ isosurface cutoff 
0.02 filename_den.cub map filename_esp.cub is added, blue text appears with 
cutoff 0.0.

Typing $ write isosurface filename.jvxl gives only a return of the prompt $. No 
jvxl file is written. Multiple entries do not work. Jmol.jar must be closed and 
reopened to make an entry. Still no positive result.

I have taken jmol.jar from jmol-14.2.9_2014.11.23 and put it in 
jmol-14.6.4_2016.10.02. It works but places the file in the former Jmol folder. 
I can redirect the jvxl file with write isosurface /Users/…/filename.jvxl.

But this not an advantage. 

Is there a problem with jmol.jar in mol-14.6.4_2016.10.02?

Thanks for your help, Fred Ziegler
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