Re: [Jmol-users] Jmol 14.20.2 - replaces 14.20.1

[Bruce Tattershall]

Thanks Bob

I haven’t been able to break the JSMol chirality finder using Chrome in a 
Windows 7 PC nor using
Firefox 52.2 in Linux, in this version, in contrast to version 14.20.1, so we 
are another step
forward.

However it still fails as before in IE11 or in Firefox 22 in a PC.
To avoid any possibility of cache trouble, I used two different other user ids 
and a public PC rather than
my office one and my own id.

The error message in Firefox is still
RangeError:  arguments array passed to Function.prototype.apply is too large

I was testing it on my P5S2Br molecule, but got the same error message on 
others of my website molecules,
if they required the use of Rule 4b.

Is it failing because these are older implementations of HTML5 and it is trying 
to use a newer feature?

I suppose there might be a common university web cache which all of our 
machines are going through,
and over which I have no control, but I do not know that.

   Bruce

From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: 10 July 2017 23:23
To: jmol-users@lists.sourceforge.net
Subject: [Jmol-users] Jmol 14.20.2 - replaces 14.20.1

Jmol.___JmolVersion="14.20.2" // 2017.07.09

bug fix: CIPChirality adding presort for Rules 4a and 4c (test12.mol; 828 lines)
bug fix: write SDF and write MOL do not set atom parity field
bug fix: JavaScript JSmol broken for chirality due to bug in Clazz.clone(obj)

bug fix: Upgrade of natural abundance average masses (no significant changes 
here):

  // all numbers except radionuclides from:
  // Atomic weights of the elements 2013 (IUPAC Technical Report)
  // Juris Meija, Tyler B. Coplen, Michael Berglund, Willi A. Brand, Paul De 
Bièvre,
  // Manfred Gröning, Norman E. Holden, Johanna Irrgeher, Robert D. Loss, 
Thomas Walczyk,
  // Thomas Prohaska  Published Online: 2016-02-24 | DOI: 
https://doi.org/10.1515/pac-2015-0305
  // 
https://www.degruyter.com/view/j/pac.2016.88.issue-3/pac-2015-0305/pac-2015-0305.xml

/* 1 H */ 1.008f, 4.002f,
/* 2 Li */ 6.9675f, 9.012f,  10.8135f, 12.0106f, 14.006f, 15.999f, 
18.998f, 20.1797f,
/* 3 Na */ 22.989f, 24.307f, 26.981f, 28.084f, 30.973f, 32.059f, 
35.4515f, 39.948f,
/* 4 K */ 39.0983f, 40.078f, 44.955f, 47.867f, 50.9415f, 51.9961f, 54.938f, 
55.845f, 58.933f, 58.6934f, 63.546f, 65.38f, 69.723f, 72.63f, 74.921f, 78.971f, 
79.904f, 83.798f,
/* 5 Rb */ 85.4678f, 87.62f, 88.905f, 91.224f, 92.906f, 95.95f, 98.91f, 
101.07f, 102.905f, 106.42f, 107.8682f, 112.414f, 114.818f, 118.71f, 121.76f, 
127.6f, 126.904f, 131.293f,
/* 6 Cs, Ba, actinides */132.905f, 137.327f, 138.905f, 140.116f, 140.907f, 
144.242f, 144.9f,  150.36f, 151.964f, 157.25f, 158.925f, 162.5f, 164.93f, 
167.259f, 168.934f, 173.054f, 174.9668f,
/* 6 Hf */  
178.49f,180.947f,183.84f,186.207f,190.23f,192.217f,195.084f,196.966f,200.592f,204.3835f,207.2f,208.98f,210f,
 210f, 222f,
/* 7 Fr, Ra, lanthanides */ 223f, 226.03f, 227.03f, 232.0377f, 231.035f, 
238.028f, 237.05f, 239.1f, 243.1f, 247.1f, 247.1f, 252.1f, 252.1f, 257.1f, 
256.1f, 259.1f, 260.1f,
/* 7 Rf - Mt */ 261f, 262f, 263f, 262f, 265f, 268f




--
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] Jmol 14.20.1

[Bruce Tattershall]

Thanks Bob

The CIPChirality additional Rules feature now works in Jmol.jar and in the 
Jmol_S java applet in
IE11 or in Firefox 22.0 in Windows 7 or in Firefox 52.2 in Linux.

As before (version 14.18.1), it still works in the JSmol HTML5 applet in Chrome 
in Windows 7 or
in Firefox 52.2 in Linux.

However, it still does not work in the JSmol applet in IE11 nor in the JSmol 
applet in Firefox 22.0 in
Windows 7.I have emptied the respective caches, and the JSmol version is 
shown as
14.20.1.
The error message (in Firefox) is still, as before,
RangeError:  arguments array passed to Function.prototype.apply is too large
If one accepts this message twice, the Rule 1a chiralities only are shown, not 
the rule 4b chiralities,
as was the case in version 14.18.1

For a bigger molecule with some 4b chirality, JSmol also fails in Chrome or in 
Firefox in Linux, with a message
script ERROR:  TypeError:  Cannot rad property ‘intValue’ of null  
J.shape.Labels
set label

  Bruce

From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: 07 July 2017 01:46
To: jmol-users@lists.sourceforge.net
Subject: [Jmol-users] Jmol 14.20.1

Download Jmol-14.20.1-binary.zip (69.7 MB) 


Jmol.___JmolVersion="14.20.1"

new feature: BZ2 compressed file reader
  -- uses org.apache.tools.bzip2.CBZip2InputStream v. 1.9.6
  -- Apache license

bug fix: ADF reader not accepting Xx.name atom ids

bug fix: SMILES generator can show wrong @/@@ or stereochemical type for some 
allenes and cumulenes

bug fix: CIPChirality additional Rules 1b, 4b, and 4c fixes (substituted 
cubanes; multiple branched branches; 841 lines)



--
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] Jmol 14.18.1

[Bruce Tattershall]

Bob

I have emptied both the Java cache in my PC and the browser cache (IE11 with 
java plugin), and get
exactly the same behaviour from the Jmol_S applet.   I get the same error 
message if I try
label %[cipRule]
and no labels are produced.Normal default atom labelling works as usual, so 
the error seems to be in the
chirality stuff.

If I use the JSmol applet, I get a different behaviour in IE11.   I get a 
message box saying
RangeError: Argument list too large to apply
This message comes up twice.   After OKing it for the second time, the 
chirality labels appear only on the
rule 1a atoms.

A following
label %[cipRule]
command then works straightaway, but still labels only the rule 1a atoms.

If, after refresh, I give the two commands in the opposite order, I still get 
the two error messages on the
first command, and no error messages on the second.   The labelling each does 
is the same for each,
whatever the order.

JSmol in Firefox in the PC gives a bit more explicit error message:
RangeError:  arguments array passed to Function.prototype.apply is too large
Otherwise its behaviour is the same as in IE11.

Jmol_S in Firefox with Java plugin fails in the same way as IE11 with Java, 
either using
Firefox in the PC or Firefox in Linux.

JSMol in Firefox in Linux works fine, as does JSMol in Chrome in the PC.
I guess that you may have used one of these for your tests.

As for Jmol.jar as an application in Linux, I was able to get some more 
information from the
Java Jmol Console.
It seems to show that the cache had been emptied, twice, and that loading of 
the model was normal.
When I gave the
label %[chirality]
command, the Java Jmol Console then showed a considerably more explicit error 
message series, which
I send as a DOS text attachment.
As I said yesterday, no labels were produced.

Bruce

From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: 08 June 2017 04:35
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Jmol 14.18.1

You will have to clear your cache.

On Wed, Jun 7, 2017 at 11:43 AM, Bruce Tattershall 
<bruce.tattersh...@newcastle.ac.uk<mailto:bruce.tattersh...@newcastle.ac.uk>> 
wrote:
Sorry Bob, but this version fails to do any chirality labelling for me, for 
either of my two models which you
looked at yesterday.
The following is copied from the Jmol Script Console:

label %[chirality]

script ERROR: java.lang.AbstractMethodError: 
org.jmol.modelset.Atom.getEdges()[Lorg/jmol/util/SimpleEdge; 
org.jmol.shape.Labels set label

Bruce

From: Robert Hanson [mailto:hans...@stolaf.edu<mailto:hans...@stolaf.edu>]
Sent: 07 June 2017 14:15
To: jmol-users@lists.sourceforge.net<mailto:jmol-users@lists.sourceforge.net>
Subject: [Jmol-users] Jmol 14.18.1

Jmol.___JmolVersion="14.18.1"  // 2017.06.06

Jmol-14.18.1-binary.zip (69.8 
MB)<https://sourceforge.net/projects/jmol/files/latest/download?source=files>

new feature: WRITE SDF writes > < user data
 -- can be set using   MODEL PROPERTY "molData" x  where x is an associative 
array
 -- can be read using _M.molData

new feature: associativeArray.pop() -- clears associativeArray

new feature: assArray1.push(assArray2) -- adds all key/value entries in 
assArray2 to assArray1.

new feature: assArray1 + assArray2  -- adds all key/value entries into a new 
associative array. (Complements a1 - a2)

bug fix: CIP misses Rule 4b cases where a branching atom has R or S chirality.
 -- see test_bt_P4.mol and test_bt_O3.mol (BH64.65 and BH64.66)
 -- see AY236.179 (3D structure was diasteriomer, so I missed that)

bug fix: WRITE MOL should not generate >  because it is  
not SDF format
bug fix: WRITE SDF should generate >  with a trailing 
space

bug fix: (SMILES) targetString.find("SMILES",patternString) will fail for 
.[C@H]2 (new group and attached to a connection number)
bug fix: SHOW CHEMICAL SMILES fails when logLevel is set > 4





--
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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--
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
vwr handling error condition: java.lang.AbstractMethodError: 
org.jmol.mo

Re: [Jmol-users] Jmol 14.18.1

[Bruce Tattershall]

Sorry Bob, but this version fails to do any chirality labelling for me, for 
either of my two models which you
looked at yesterday.
The following is copied from the Jmol Script Console:

label %[chirality]

script ERROR: java.lang.AbstractMethodError: 
org.jmol.modelset.Atom.getEdges()[Lorg/jmol/util/SimpleEdge; 
org.jmol.shape.Labels set label

Bruce

From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: 07 June 2017 14:15
To: jmol-users@lists.sourceforge.net
Subject: [Jmol-users] Jmol 14.18.1

Jmol.___JmolVersion="14.18.1"  // 2017.06.06

Jmol-14.18.1-binary.zip (69.8 
MB)

new feature: WRITE SDF writes > < user data
 -- can be set using   MODEL PROPERTY "molData" x  where x is an associative 
array
 -- can be read using _M.molData

new feature: associativeArray.pop() -- clears associativeArray

new feature: assArray1.push(assArray2) -- adds all key/value entries in 
assArray2 to assArray1.

new feature: assArray1 + assArray2  -- adds all key/value entries into a new 
associative array. (Complements a1 - a2)

bug fix: CIP misses Rule 4b cases where a branching atom has R or S chirality.
 -- see test_bt_P4.mol and test_bt_O3.mol (BH64.65 and BH64.66)
 -- see AY236.179 (3D structure was diasteriomer, so I missed that)

bug fix: WRITE MOL should not generate >  because it is  
not SDF format
bug fix: WRITE SDF should generate >  with a trailing 
space

bug fix: (SMILES) targetString.find("SMILES",patternString) will fail for 
.[C@H]2 (new group and attached to a connection number)
bug fix: SHOW CHEMICAL SMILES fails when logLevel is set > 4





--
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
--
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] saving and retrieving orbital surfaces working well with JSmol

[Bruce Tattershall]

I am pleased to say that the new facilities for saving and retrieving orbital 
surfaces or contour plots
on a plane, available from version 14.15.2, seem to work well for me.

My webpage 
https://www.staff.ncl.ac.uk/bruce.tattershall/structs/p5e2x.php
for the molecule P5 S2 Cl offers the ability to view the through-space overlaps 
of four NBOs.
Either orbital surface models, or contour plots on a plane, or both 
superimposed, may be viewed.   
Each of the four NBOs may be switched on or off individually, so that the user 
may unravel in their mind the
somewhat complex overall picture of lone-pair repulsions.

If you wish to see this, select the p5s2cl button, then, in the p5s2cl Model 
window which pops up,
select the NBO overlaps button.

Previously, I implemented this by reading in the PNBO file .36 from an NBO 
analysis in Gaussian, and then
having Jmol calculate the required surfaces.  This went in an acceptable time 
in Java Jmol_S using e.g.
Java-enhanced IE11, but took impossibly long using HTML5 JSmol in e.g. Chrome 
(several minutes).

Now, using version 14.15.2 Jmol_S to write .jvxl and .pmesh files respectively, 
compressing the .pmesh
files using gzip, and reworking the web page to read these back in instead of 
calculating from the .36 data,
the NBO overlaps page loads in 3 seconds using Jmol in IE11, or 6 seconds using 
JSMol in Chrome,
which I think is very acceptable and useful.

Thanks Bob!

One trouble with updating one's web pages to use a new feature in Jmol or 
JSmol, is that, after installing a
new version of Jmol, returning users may find that one's pages crash because 
incompatible dynamically loaded
bits of the Jmol library from the old version are still lurking in their 
browser caches.  Clearly, they need to
empty their browser memory if they know how to, but the error messages, coming 
e.g. from the HTML5
implementation in Chrome, do not indicate this.  
I guess that an answer would be to give JmolFolder a different name, changing 
with the version, but this would
mean going through all the web pages and changing the reference to it, which is 
an error-prone process.


  Bruce

Dr. Bruce Tattershall, School of Chemistry, Newcastle University, England


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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
--
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
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Re: [Jmol-users] Jmol 14.14.1 contour isosurfaces as .pmesh files

[Bruce Tattershall]

Dear Bob

I have been trying out your new .pmesh feature.  It works well for me, both in 
JSmol and in Jmol_S.

Thanks very much:   that solves my timing problems with orbital contour plots 
in a plane, and  I will work
on converting the web pages concerned to read in pre-saved isosurfaces instead 
of calculating them
from the orbital data.   I will read contours from .pmesh files and orbital 
surfaces from .jvxl files.

The only thing I noticed was that the .pmesh files were rather large at half a 
megabyte each, for pretty small
orbitals with only 21 contours, extending over about 5 Angstroms each.  I found 
that these could be
compressed using gzip to about 140 kB, and Jmol_S or JSmol would still read 
them without obviously more
delay.

I just wonder whether all that precision is necessary, for models which are 
only going to be assessed by eye,
relatively quickly.I don’t know how easy it is to control numeric output 
format in the languages you are
using, or whether lower precision would be compatible with existing routines 
for reading .pmesh files.

It just occurred to me that if one was going to use this method a lot, it would 
save server file space
and users’ downloads if the files could be a bit smaller.

Thanks again

Bruce

From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: 20 April 2017 16:47
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Jmol 14.14.1

OK - this is better:  Looking for the latest version? Download 
Jmol-14.14.1-binary.zip (69.7 MB) 


On Wed, Apr 19, 2017 at 11:35 PM, Robert Hanson 
> wrote:
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: 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


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Re: [Jmol-users] Jmol 14.14.1 chirality

[Bruce Tattershall]

Dear Bob

The chirality calculation is clearly useful.

I have tried it on my chiral phosphorus compounds, e.g. as in
https://www.staff.ncl.ac.uk/bruce.tattershall/structs/bpthiq.php
and it finds the chiral carbons in the organic ligands and successfully labels 
them (as R in this case),
but it does not find the chirality of the phosphorus atoms to which they are 
attached.

I have no idea of how this works, but would it be possible to extend it easily 
to phosphorus chirality (for which
one uses the same rules but counts the lone pair as lowest priority)?

When I first got into measuring NMR spectra of diastereomers of such compounds 
about 15 years ago,
I found it very hard to get my inorganic chemist’s head around the chirality 
implications.  It would
have been very useful to have a tool to work it out for me.

If you are going to elements other than carbon, then I guess that besides 
phosphorus, the inorganic
chemist’s favourite, the chirality at silicon, germanium and arsenic could also 
be useful to people.

Best wishes

   Bruce

Bruce Tattershall
School of Chemistry
Newcastle University
England

From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: 20 April 2017 16:47
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Jmol 14.14.1

OK - this is better:  Looking for the latest version? Download 
Jmol-14.14.1-binary.zip (69.7 MB) 
<https://sourceforge.net/projects/jmol/files/latest/download?source=files>

On Wed, Apr 19, 2017 at 11:35 PM, Robert Hanson 
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>> wrote:
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 
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>> 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)


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[Jmol-users] JSmol applet creation of mo surfaces or contour plot is slow

[Bruce Tattershall]

Over the last couple of years I have created a number of web  pages using Jmol, 
to support research
publications in inorganic main-groups chemistry or for undergraduate teaching.

I have created a portfolio web page
https://www.staff.ncl.ac.uk/bruce.tattershall/jmolapps/portfolio.html
showing six different  examples of these, to try to encourage my colleagues to 
do likewise, but 
I have to start by telling them to use a Java-enabled browser.   It would be 
much better if I didn't need to.

All of my web pages offer the user a choice of using the Java Jmol applet or 
the HTML5.0 JSmol applet,
implemented using the concatenation of JSmol.min.js and Jmol2.js as recommended 
in 
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object
and patching the value of use in the Info variable for 
Jmol.getApplet("JmolApplet0", Info)
accordingly.

For all of my web pages, using IE11 and the Java plugin, and taking my offered 
Java Jmol applet option,
works excellently, producing  Jmol_S models.
 
 Firefox for Windows with the Java plugin is also fine.

Moving to Chrome and necessarily taking the HTML5.0 JSmol applet option also 
works very well for models
of molecular geometry, including reaction path animations.  

However, models of orbital surfaces, or contour plots of orbitals on a plane, 
are much too slow to load.
An example is provided from
https://www.staff.ncl.ac.uk/bruce.tattershall/teaching/chy135/co2mo/co2.php
in which MOs for CO2 may be picked from an energy level diagram.   This calling 
page is fine with either applet,
but the called page which generates the model for the chosen MO, is not.  An 
example, with the query string
set for HTML5.0 JSmol use, is 
https://www.staff.ncl.ac.uk/bruce.tattershall/teaching/chy135/co2mo/showjmol.php?use=HTML5=co2=MO=sigma_C(2p)O(2p)=9=1

In Chrome, this takes 20 seconds, and about the same in Firefox (compared with 
4 seconds for the
Java Jmol applet option), while IE11 takes 35 seconds, in each case running in 
a dual core 2.93GHz 32-bit PC
running Windows 7.   
(IE11 without Java is unacceptable anyway because its mouse response in 
rotating models is too slow and jerky,
for any kind of model.) 

The orbital data comes from an NBO calculation, so the orbital distribution is 
calculated entirely 
within the applet.   By calling the functions to calculate an mo surface or to 
calculate a contour plot on the yz
plane, from a LoadStructCallback function, I can ensure that the data loading 
is done only once.  
Putting on breakpoints in a debugger shows that this is not the time-consuming 
part.   It appears to be that it is
calculating the mo surface which is taking the bulk of the time.

I should be very happy if someone more expert in using JSmol could look at the 
page source of the example
above, and let me know if I am doing something poorly.  The .php script is only 
doing the obvious in
interpreting the query string:  everything of consequence in using JSmol is 
visible in the delivered 
HTML/Javascript page source.

Thanks
   Bruce Tattershall
  School of Chemistry, Newcastle University, England





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