[Jmol-users] Add atom from command line

[Donna Pergin]

So sorry to bother all of you, but I have searched in vain for this. Is it 
possible to add an atom from the command line (say, to a selected atom)? If so, 
where is the reference for that?
Thanks,
Donna Perygin--
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Re: [Jmol-users] Jmol 14.15.1

[Bruce Tattershall]

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
--
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[Jmol-users] Fwd: Important MathJax Information

[Robert Hanson]

FYI

-- Forwarded message --
From: Timothy Wallace 
Date: Fri, Apr 28, 2017 at 12:20 PM
Subject: Fwd: Important MathJax Information



On April 30th MathJax are closing their self-hosted CDN (Content Delivery
Network) services at *cdn.mathjax.org * and
*beta.mathjax.org
*. If your colleagues are linking to either of
these CDNs for MathJax functionality in any web pages/applications, they
will need to change the link(s) to point to an alternative CDN provider.
This should be a minor change and details on carrying this out are provided
below.


*Changing MathJax CDN: *We recommend changing to the cdnjs CDN. MathJax are
working with cdnjs to push out future releases.

You need to change the link to the CDN wherever it appears in your web
page/application code. For example, if you have been using the latest
MathJax version (v2.7.0) change the link text before the question mark as
below. Note that the url parameters (everything including and after the
“?”) should not be changed:

https://cdn.mathjax.org/mathjax/2.7-latest/MathJax.js
<https://cdn.mathjax.org/mathjax/2.7-latest/MathJax.js?>*?
<https://cdn.mathjax.org/mathjax/2.7-latest/MathJax.js?>...">
to
https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js
<https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?>*?
<https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?>
...">

This only applies where the CDN is being used to include MathJax
functionality. If the MathJax library is being used locally (i.e. has been
downloaded and linked to), then no change is required.

For further details, please see:
https://www.mathjax.org/cdn-shutting-down/
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Re: [Jmol-users] Add atom from command line

[Angel Herráez]

Hi Donna

You could probably use

set appendNew false
load append data ..

See
https://chemapps.stolaf.edu/jmol/docs/#set_appendnew
https://chemapps.stolaf.edu/jmol/docs/#loadappend
https://chemapps.stolaf.edu/jmol/docs/#loaddata
https://chemapps.stolaf.edu/jmol/docs/#data



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Re: [Jmol-users] Jmol 14.15.1

[Robert Hanson]

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
--
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Re: [Jmol-users] scripting syntax

[Angel Herráez]

[I'm moving this to the jmol-users list]

Hi Jeff

I foresee no problem in your scripts.

My advice is that you right-click and open the Console, then paste there your 
scripted commands one at a time and see which one gives the error or fails 
to work.



On 28 Apr 2017 at 15:15, Jeff Sims wrote:

> I´m trying to diagnose scripts written a few years ago that are no longer 
> working in the latest version of JSmol.
> The same scripts work correctly in an older version of JSmol: ver. 14.2.4 
> (2014-08-03).
> After updating JSmol, there is no error in the JSmol console, just a blank 
> JSmol canvas (no atoms appear).
> 
> I suspect that it´s syntax related to `select´? because nothing is being 
> selected for color or style, but not sure.
> 
> Here are a few excerpts: (I´ll just include an example of each type of call). 
> Does any of this look problematic or need fixes?
> I can post the full scripts if helpful.
> 
> model 1
> rotate z -108
> rotate y 130
> rotate z 32
> zoom 100
> restrict not :a and not solvent
> 
> select 147-157 and :a
> define switch1a selected
> 
> select switch1a or switch2a or switch3a 
> define allswitcha selected
> 
> select :i and (177,179,181,192,198,199,200,202,205,211)   
> #numbers are less by 1 than those in the Nature 379 article
> define ihb selected   
> #alpha subunit residues hbonding with beta
> 
> elect (switch1b and backbone) and not (173-176)   #these 
> sw1b residues interact w/beta
> select selected or (177,179,181) and :i
> define subset1b selected
> 
> select :a and (172,173,174,176,179,185)or (switch2a and backbone)
> define subset2a selected
> 
> select :a
> color [xFFAD00]   #orange
> 
> select gtp
> color [x00C000]   #guanine green
> 
> select gdp
> color [xFF]
> 
> select :i or :b or :g or :d
> spacefill on
> select atomno=644 and :i
> label "\u03b1"
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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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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Re: [Jmol-users] Jmol 14.15.1

[Robert Hanson]

Fred, what's your story? I'm reading and writing Gaussian cube files.
Example?

On Fri, Apr 28, 2017 at 3:29 PM, fziegler 
wrote:

> 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 <
> bruce.tattersh...@newcastle.ac.uk> 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
>
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
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> Jmol-users@lists.sourceforge.net
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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
--
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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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