[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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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

[Robert Hanson]

On Fri, Apr 21, 2017 at 11:10 AM, Bruce Tattershall <
bruce.tattersh...@newcastle.ac.uk> wrote:

> 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.
>
>
It's a work in progress.

Limitations:

 no parallel chirality paths
 not processing inositols correctly
 no lone-pair business
 standard E/Z, R/S, r/s only; no allenes, no planar asymmetry



>
> 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)?
>
>
Lone pairs wouldn't be too difficult to add, particularly if they are
limited to P and S. They are definitely in the IUPAC 2013 spec. I'd like to
add imine stereochemistry as well.



>
>
> 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.
>

Silicon and ammonium are just like carbon, I think. As and P no problem.

Definitely not going to higher valencies any time soon.

Higher priorities are allenes and getting the darned inositol business
working  correctly. But maybe P and S and As are so easy I should just do
them

Bob
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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) 


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: 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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Re: [Jmol-users] Jmol 14.14.1

[Pshemak Maslak]

I can confirm: the command (in bold below) generated the expected closed 
CAP surfaces in Jmol and JSmol.


Thanks Bob,

PM


On 4/20/2017 10:34 PM, Robert Hanson wrote:



On Thu, Apr 20, 2017 at 8:35 AM, Pshemak Maslak > wrote:


Bob;

I am looking forward to exploring the new R/S and E/Z
functionality; it's a great addition.

Does this version include fix for "/*spacefill ionic;lcaocartoon
scale 1.0 CAP unitcell "cpk";spacefill off" */which freezes the
Jmol (Java) and leaves open surfaces (no "cap') on many unticell
faces in JSmol?


yes, I think so. Please test. Also the fact that sometimes caps were 
not completely closed.


Thanks,

PM




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Re: [Jmol-users] Jcamp-mol setup

[PASCAL Andrew]

Looks great, thanks Bob.



andy pascal (andrew.pas...@cea.fr)

From: PASCAL Andrew
Sent: 13 April 2017 15:21
To: jmol-users@lists.sourceforge.net
Subject: [PROVENANCE INTERNET] Re: [Jmol-users] Jcamp-mol setup


That would be great! I'm animating a carotenoid, which is long and thin, so it 
looks better if it can take the full width of the screen (I want to use it in 
seminars to illustrate Raman vibrations).



On a side note - I seem to have a problem keeping JSpecView properties between 
sessions. Anything I change is kept if I close and reopen JSV in the same Jmol 
session, but lost once Jmol is closed and reopened. It also ignores anything I 
put in Options/Préférences, or into jspecview.properties by hand.



andy pascal (andrew.pas...@cea.fr)

From: Robert Hanson [hans...@stolaf.edu]
Sent: 13 April 2017 15:11
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Jcamp-mol setup

That said, it's a very good idea, and I'm sure very easy to implement.

On Thu, Apr 13, 2017 at 8:11 AM, Robert Hanson 
> wrote:
no, there isn't, but you can adjust the size of that window to anything you 
want just be dragging the bars around it or resizing the window.

On Wed, Apr 12, 2017 at 2:24 PM, PASCAL Andrew 
> wrote:
When connecting a spectrum with a molecular animation in a JCamp-MOL file, is 
there any way to default to using the main Jmol window for the structure, 
rather than the JSpecView side panel?

Thanks,

andy pascal (andrew.pas...@cea.fr)

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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




--
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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