Re: [Jmol-users] Jmol Anniversaries?

[Rzepa, Henry S]

Tom Grey, who is listed in the Jmol hall of fame, occupied a student desk in 
the communal comp chem section where  I was, and he must have filled me in on 
the early developments.  I know that  Java was released in mid 1996, and apps  
started emerging in 1997. Perhaps  Jmol was developed/gestated relatively  
“silently” during the period 1997-2001?, before it acquired a sourceforge 
presence (SF was only founded in 1999 and released for use in 2000!).  

I have literally just (re)discovered this page from 1997: 
http://www.ch.ic.ac.uk/java/   (Last Update: 
August 11, 1997) which lists a whole bunch of java applets developed around  or 
less than a year since the language was released by Sun.  

This one, http://www.ch.ic.ac.uk/java/applets/f2m2f/ 
  was written around August 1996 by 
a french student Guillaume Cottenceau  visiting London, and it still works!   I 
wonder what happened to him?

This one http://www.ch.ic.ac.uk/local/nmr/   
comes from August 1997  and contains NMR and MS spectral viewers which also 
still work!

So despite all the security issues etc, 20 year old  Java is still capable of 
running! 

My reason for posing the question "Jmol Anniversaries?”  is that  I thought the 
20th anniversary might have been approaching.   Perhaps indeed it has? (PS the 
server http://www.ch.ic.ac.uk   started operation in 
August 1993 and probably contains a treasure trove of historical items which 
might reveal an answer?)

Henry Rzepa, http://orcid.org/-0002-8635-8390




> On 7 Jun 2017, at 09:26, C Anthony Lewis  wrote:
> 
> Hi Henry,
>  
> I guess the jmol-user list archive 
> (https://sourceforge.net/p/jmol/mailman/jmol-users/ 
> ) might help with dates 
> for at least the last two. I note this archive goes back to 18/4/2001 at this 
> location, with the first message being one from you. However, this seems to 
> be a follow-up to an earlier message but I’m not sure where earlier messages 
> are archived, although I may have saved something locally.
>  
> Anthony
>  



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Re: [Jmol-users] display of contacts in two frames/models

[Robert Hanson]

definitely a bug.
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Re: [Jmol-users] display of contacts in two frames/models

[Robert Hanson]

Not a bug. You just have to be careful to use the ID and atom selection
carefully

load =1blu
contact ID c1 {SF4}
load append =1d66
contact ID c2 {nucleic and 2.1}

If you leave off ID, then the two have the same default id, "contact1", and
so the first is lost when the second appears.
If you leave off "and 2.1", then you risk picking up contacts between the
two models or within the first.



On Sat, Jun 10, 2017 at 10:06 AM, Robert Hanson  wrote:

> definitely a bug.
>



-- 
Robert M. Hanson
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] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Robert Hanson]

I think it gets back to the issue of what is embedded in what. The magic of
the Jmol applet, of course, is that you can embed it in whatever context
you want -- Jena3D, for example. This is not directly possible for the Jmol
application. (It can be done, but you have to be a Java programmer to do
it.) So I am not seeing a solution for people who want to embed the Jmol
applet in a larger context. JavaFX is the other way around -- embed a web
page in a devoted Java project.

Bob

​
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Re: [Jmol-users] display of contacts in two frames/models

[Angel Herráez]

Oh, thanks Bob

I should have known, since contacts are a kind of isosurface!  I knew ID is 
essential to have several at a time, but I missed that bit now.

This is going to look great!

Thanks


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Re: [Jmol-users] cloning part of a model into another frame

[Robert Hanson]

You might not get all the information in a PDB file, but I think you could
select the atoms and append them:

load =1blu
select sf4
x = write("PDB")
load append inline @x

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