Re: [Jmol-users] More on NIH Resolver

[Otis Rothenberger]

  Bob,

I thought the taxol problem with the gif generation that I referenced 
below was the aromatic lower case issue I asked about earlier. Now I 
think not. The Resolver has translated other Jmol smiles with lower case 
Kekule aromatics correctly. It definitely can create the gif for taxol 
when this is addressed directly in the Resolver Web page. When I look at 
the SMILES that Jmol creates for taxol, I get the following:

print {*}.find('SMILES');
c1...@](C)3[C@@H](O)C[C@@h]...@]15oc(C)=O.[C@@h]2...@](O)7C(C)(C)C8=C(C)[...@h]9oc%10=o.c79.c%118c3=o.o%11c(C)=o.o6c%12=o.c%12%13=cc=cc=c%13.c5o4...@h](O)%10[C@@H]%14c%15=cc=cc=c%15.N%14C%16=O.c%16%17=cc=cc=c%17

Resolver produces:

CC(=O)o...@h]1c(=O)[...@]2(C)[C@@H](O)c...@h]3oc[c@@]3(OC(C)=O)[...@h]2[c@H](OC(=O)c4c4)[...@]5(O)c...@h](OC(=O)[...@h](O)[C@@H](NC(=O)c6c6)c7c7)C(=C1C5(C)C)C


I'm guessing that Resolver can't deal with the 2 digit ring (or fragment) 
closure notation - i.e % notation.

Otis

Otis Rothenberger
chemagic.com


On 9/2/2010 10:24 PM, Otis Rothenberger wrote:
>The NIH Resolver will generate a gif image of the Lewis line structure
> of a submitted SMILES. I ignored this feature because I thought it was
> just another pretty little picture. Boy was I wrong!
>
> A JavaScript construct of the following form:
>
> var tempStr = " src='http://cactus.nci.nih.gov/chemical/structure/"; + escape(jmolSmiles)
> + "/image' />";
>
> sz = desired gif size
> jmolSmiles = an evolving model kit mode model.
>
> When rendered the above gif not only has appropriate bond wedges. The
> chiral carbons are conveniently labeled R or S
>
> If you want to see a quick demo of this, go to
>
> http://chemagic.com/web_molecules/script_page_large.aspx
>
> The default model will be just fine. Click The Molecular Editor Link;
> click the Image link, click the NIH 2D Capture link.
>
> We edit models using our own Edit screen interface rather than the Jmol
> native interface. Play with editing, and you'll see that Resolver gets
> it right. You need to click the image capture link each time.
>
> There are some problems with complex aromatics (e.g. taxol), but I'm
> working on this problem.
>
> Otis
>



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Re: [Jmol-users] Jmol and crystallography: the paper

[Eran Hodis]

 Kudos!




__

>From Robert Hanson 
Sent Thu 9/2/2010 10:21 PM
To jmol-users@lists.sourceforge.net
Subject [Jmol-users] Jmol and crystallography: the paper




This just in!


J. Appl. Cryst. (2010). 43  [ doi:10.1107/S0021889810030256 
(http://dx.doi.org/10.1107/S0021889810030256) ]Jmol - a paradigm shift in 
crystallographic visualization
R. M. Hanson 
(http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Hanson%2C%20R%2EM%2E)


Synopsis: Features of Jmol that allow new ways for students to interact with 
three-dimensional virtual models and explore molecular and crystallographic 
symmetry are described.

Online 1 September 2010
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr (http://www.stolaf.edu/people/hansonr)
phone: 507-786-3107


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] More on NIH Resolver

[Otis Rothenberger]

  The NIH Resolver will generate a gif image of the Lewis line structure 
of a submitted SMILES. I ignored this feature because I thought it was 
just another pretty little picture. Boy was I wrong!

A JavaScript construct of the following form:

var tempStr = "";

sz = desired gif size
jmolSmiles = an evolving model kit mode model.

When rendered the above gif not only has appropriate bond wedges. The 
chiral carbons are conveniently labeled R or S

If you want to see a quick demo of this, go to

http://chemagic.com/web_molecules/script_page_large.aspx

The default model will be just fine. Click The Molecular Editor Link; 
click the Image link, click the NIH 2D Capture link.

We edit models using our own Edit screen interface rather than the Jmol 
native interface. Play with editing, and you'll see that Resolver gets 
it right. You need to click the image capture link each time.

There are some problems with complex aromatics (e.g. taxol), but I'm 
working on this problem.

Otis

-- 
Otis Rothenberger
chemagic.com




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Re: [Jmol-users] Jmol and crystallography: the paper

[Whitwell, George]

Congratulations!  I enjoyed reading the preprint before BCCE.
George

From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: Thursday, September 02, 2010 3:22 PM
To: jmol-users@lists.sourceforge.net
Subject: [Jmol-users] Jmol and crystallography: the paper


This just in!

J. Appl. Cryst. (2010). 43  [ 
doi:10.1107/S0021889810030256 ]

Jmol - a paradigm shift in crystallographic visualization
R. M. 
Hanson

Synopsis: Features of Jmol that allow new ways for students to interact with 
three-dimensional virtual models and explore molecular and crystallographic 
symmetry are described.

Online 1 September 2010

--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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 downloads top 400,000

[Michael Evans]

Oh man, this number is only going to grow!

On Thu, Sep 2, 2010 at 2:28 PM, Robert Hanson  wrote:

> Just noticed that there have been over 437,000 downloads of Jmol. Wow!
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
>
>
> --
> This SF.net Dev2Dev email is sponsored by:
>
> Show off your parallel programming skills.
> Enter the Intel(R) Threading Challenge 2010.
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>


-- 
Mike Evans
Organic Chemistry Graduate Student
Moore Group
University of Illinois, Urbana-Champaign
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Re: [Jmol-users] Find SMILES problem

[Otis Rothenberger]

 Bob,

The ring is flat, but it has two sp3 carbons (CH2's). To make sure this 
was not associated with my post model change processing, I reproduced 
the effect by building benzene from methane followed by 
1,3-cyclohexadiene formation at:


http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm

I get the same results.

My issue is fairly localized to one problem, and I'd be hesitant to 
change Jmol in a way that might create more problems down the road for 
this one problem. At this point, the only thing this issue is fouling is 
using NIH Resolver as a "minimization" tool. It keeps returning benzene 
on some modified benzene queries - most notably 1,3-cyclohexadiene.


I'm experimenting with

escape(jmolSmile.replace(/c/ig, 'C'))

on this type of query only - i.e. NIH Resolver "minimize."

I'm not sure that I'd even call this a work around since there is 
nothing wrong with Jmol smiles. Playing around with benzene and pyridine 
indicates that this approach is working. Even though I do not change "n" 
in the 2,3-dihydropyridine query, the Resolver reads in correctly and 
returns the correct SMILES and model.


The lower case Kekule aromatic SMILES will play havoc with asymmetric 
"compares" - JME/Jmol & NIH/Jmol. But I'm not sure these asymmetric 
"compares" are an issue, just a nuisance in constructing an internal 
data base. In this latter case, one has to hand convert JME SMILES (for 
example) to lower case aromatic.


Otis

Otis Rothenberger
chemagic.com


On 9/2/2010 3:09 PM, Robert Hanson wrote:



On Thu, Sep 2, 2010 at 9:17 AM, Otis Rothenberger 
mailto:osrot...@chemagic.com>> wrote:


Bob,

Thanks. Your explanation of what aromatic means is the key here. I
see now why this is happening. If I start with benzene and make
1,3-cyclohexadiene, then it ends up in flat energy minimum that
"minimize" does not change. I always get the lower case smiles. If
I use "drag" to pull it out of shape, then I get upper case. If I
make cyclohexene from benzene, "minimize" eventually get it and
twists a bit. Once it twists, I get upper case.

One thing here is that it looks like the statement "aromatic just
means flat and all sp2 for Jmol" is not quite correct. Flat seems
to be a sufficient condition.


then there's a bug. You sure you have a tetrahedral center? -- not 
just "square planar but distorted square planar"?



The context here may seem strange, but we are working on student
model kit exercises, and we want the Jmol model kit to allow the
same kind on tactile playing that a ball and stick model kit
allows - e.g. take a double bond out of benzene. To be sure, I do
not see the problem if I make 1,3-cyclohexadiene from cyclohexane.
That should have been a clue that the flatness was the issue!

Re NIH, for all of the following, the Resolver returns benzene (no
explicit hydrogens in submitted SMILES):

Jmol lower case benzene
Jmol lowercase cyclohexadiene
Jmol lower case cylohexene
Jmol lower case cyclohexane, which is, of course synonymous with
"aromatic SMILES" for benzene.

Evidently, the Resolver is just ignoring "=" in this lower case
context.


that makes sense. What do you propose? There could be an aromatic 
option that requires explicit hydrogens:


/explicitaromatic/

  --- flat ring
  --- tricoordinate carbon
  --- all substituents in plane of ring


/aromatic/ (default)

 -- flat ring
 -- all substituents in plane of ring

I hate to think what implications it might have for heterocycles, 
though.  That's what I was trying to avoid.


Bob


Otis

Otis Rothenberger
chemagic.com  


On 9/2/2010 1:52 AM, Robert Hanson wrote:



On Wed, Sep 1, 2010 at 10:21 PM, Otis Rothenberger
mailto:osrot...@chemagic.com>> wrote:

 Bob,

There is a general aromatic problem that I'm having with find
SMILES
that's easiest to explain with a specific scenario. If I load
benzene
and run "var x={*}.find('SMILES');echo @x," I get:

c1=cc=cc=c1

If I use model kit mode to make 1,3-cyclohexadiene, the same "var
x={*}.find('SMILES');echo @x" produces

c1=cc=ccc1


I'll look into that. Almost certainly a bug. It should only use
lower case c if the ring is totally flat and there are no sp3
centers. I'm really surprised it's doing that. The code is only
supposed to insert lower case "c" when:

-- the ring is flat
-- the ring has no sp3 centers

Is it possible you are sending it a flat no-hydrogen ring? When I
use the model kit, I get:


C1==C1


I'm now stuck in lower case "c" mode on this ring no matter
what I do to
the ring. If I break a ring bond while the ring is no longer
aromatic
and reform the bond, I go back to upper case "C"


remember -- "aromatic" just means "flat and all sp2" for Jmol.
We're not going 

[Jmol-users] jmol downloads top 400,000

[Robert Hanson]

Just noticed that there have been over 437,000 downloads of Jmol. Wow!

-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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 and crystallography: the paper

[Egon Willighagen]

On Thu, Sep 2, 2010 at 9:21 PM, Robert Hanson  wrote:
> This just in!

Congrats!

Egon


-- 
Dr E.L. Willighagen
Post-doc @ Uppsala University (only until 2010-09-30)
Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

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[Jmol-users] Jmol and crystallography: the paper

[Robert Hanson]

*This just in!
*

*J. Appl. Cryst.* (2010). *43*  [
doi:10.1107/S0021889810030256]
*Jmol* - a paradigm shift in crystallographic visualization R. M.
Hanson

*Synopsis: *Features of *Jmol* that allow new ways for students to interact
with three-dimensional virtual models and explore molecular and
crystallographic symmetry are described.

Online 1 September 2010

-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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] Find SMILES problem

[Robert Hanson]

On Thu, Sep 2, 2010 at 9:17 AM, Otis Rothenberger wrote:

>  Bob,
>
> Thanks. Your explanation of what aromatic means is the key here. I see now
> why this is happening. If I start with benzene and make 1,3-cyclohexadiene,
> then it ends up in flat energy minimum that "minimize" does not change. I
> always get the lower case smiles. If I use "drag" to pull it out of shape,
> then I get upper case. If I make cyclohexene from benzene, "minimize"
> eventually get it and twists a bit. Once it twists, I get upper case.
>
> One thing here is that it looks like the statement "aromatic just means
> flat and all sp2 for Jmol" is not quite correct. Flat seems to be a
> sufficient condition.
>

then there's a bug. You sure you have a tetrahedral center? -- not just
"square planar but distorted square planar"?


>
> The context here may seem strange, but we are working on student model kit
> exercises, and we want the Jmol model kit to allow the same kind on tactile
> playing that a ball and stick model kit allows - e.g. take a double bond out
> of benzene. To be sure, I do not see the problem if I make
> 1,3-cyclohexadiene from cyclohexane. That should have been a clue that the
> flatness was the issue!
>
> Re NIH, for all of the following, the Resolver returns benzene (no explicit
> hydrogens in submitted SMILES):
>
> Jmol lower case benzene
> Jmol lowercase cyclohexadiene
> Jmol lower case cylohexene
> Jmol lower case cyclohexane, which is, of course synonymous with "aromatic
> SMILES" for benzene.
>
> Evidently, the Resolver is just ignoring "=" in this lower case context.
>
>
that makes sense. What do you propose? There could be an aromatic option
that requires explicit hydrogens:

/explicitaromatic/

  --- flat ring
  --- tricoordinate carbon
  --- all substituents in plane of ring


/aromatic/ (default)

 -- flat ring
 -- all substituents in plane of ring

I hate to think what implications it might have for heterocycles, though.
That's what I was trying to avoid.

Bob


> Otis
>
> Otis Rothenbergerchemagic.com
>
>
> On 9/2/2010 1:52 AM, Robert Hanson wrote:
>
>
>
> On Wed, Sep 1, 2010 at 10:21 PM, Otis Rothenberger 
> wrote:
>
>>  Bob,
>>
>> There is a general aromatic problem that I'm having with find SMILES
>> that's easiest to explain with a specific scenario. If I load benzene
>> and run "var x={*}.find('SMILES');echo @x," I get:
>>
>> c1=cc=cc=c1
>>
>> If I use model kit mode to make 1,3-cyclohexadiene, the same "var
>> x={*}.find('SMILES');echo @x" produces
>>
>> c1=cc=ccc1
>>
>>
> I'll look into that. Almost certainly a bug. It should only use lower case
> c if the ring is totally flat and there are no sp3 centers. I'm really
> surprised it's doing that. The code is only supposed to insert lower case
> "c" when:
>
> -- the ring is flat
> -- the ring has no sp3 centers
>
> Is it possible you are sending it a flat no-hydrogen ring? When I use the
> model kit, I get:
>
>
> C1==C1
>
>
>
>
>> I'm now stuck in lower case "c" mode on this ring no matter what I do to
>> the ring. If I break a ring bond while the ring is no longer aromatic
>> and reform the bond, I go back to upper case "C"
>>
>>
> remember -- "aromatic" just means "flat and all sp2" for Jmol. We're not
> going to get into multiple bonding issues. There's no "antiaromatic" here.
> It doesn't matter if you have 6 carbons and all single bonds or 6 carbons
> and all double bonds or 8 carbons (as in octadienyl dianion ligand). As long
> as it's flat and there aren't any tetrahedrally directed substituents, Jmol
> is going to use "c" instead of "C".
>
> Bob
>
>
>
>> There are really two issues here:
>>
>> 1) Jmol creates Kekule SMILES in lower case, and this does not seem to
>> be standard. As long as compare is Jmol/Jmol, this is not a problem. And
>> in fact, NIH Resolver which uses aromatic SMILES (c1c1), recognizes
>> the Jmol lower case Kekule SMILES for benzene.
>>
>
> It's definitely incorrect. You really have all the H atoms there and it's
> not planar?
>
>  2) Getting stuck in lower case mode, however, is a problem and seems to
>> be a bug.
>>
>> I have a feeling that calculate/reset aromatic may offer one solution to
>> the problem, but I'm not sure it can be used in a general sense to
>> "unaromatise" an aromatic ring. If this is not a bug, an alternative is
>> to use JavaScript toUpperCase() on s, c, n, and o, but that has ugly
>> side affects.
>>
>>
> See if you can find out more about what exactly the NIH server is
> requiring, if that's the issue. There's also a
>
> /noaromatic/ flag in Jmol's SMILES business that turns off aromatic
> checking. That might be useful.
>
> Help me define what the context is. Where are these being used?
>
>
>
>> Otis
>>
>> --
>> Otis Rothenberger
>> chemagic.com
>>
>>
>>
>>
>>
>> --
>> This SF.net Dev2Dev email is sponsored by:
>>
>> Show off your parallel programming skills.
>> Enter the Intel(R) Threading Challenge 2010.
>

Re: [Jmol-users] how export in fractional coordinates

[Robert Hanson]

Piero, on the first issue, I have a feeling this is a bug in the Crystal
file reader, because there's no way Jmol is combining 1.1 atoms into 1.2
atoms. Just can't happen. Do the following:

print {1.1}.length

print {1.2}.length

print {1.1 and 1.2}.length

I have a hunch the reader is copying the atoms multiple times and you are
going to see something like this:

10
20
0

(Crystal file reader bug)

But you might also get

10
20
10

(Jmol select bug)

Which is it? Please send me that file (again).

Bob


On Thu, Sep 2, 2010 at 12:57 PM, P.Canepa  wrote:

> Dear all,
>


> When I do like var xyzCoord = {1.2}.label(" %16.9[xyz]"); print xyzCoord  i
> get
>
> Fe  0.355299979 0.35539 0.35539
> Fe1  0.144699976 0.14461 0.14461
> Fe1  0.644700050 0.644700050 0.644700050
> Fe  0.85539 0.855300069 0.855300069
> O  0.555899978 0.944100022 0.25030
> O  0.24970 0.555899978 0.944100022
> O  0.944100022 0.25060 0.555900037
> O  0.444100022 0.055900037 0.75060
> O  0.75000 0.444100022 0.055900037
> O  0.055899978 0.75000 0.44403
> Fe  0.355299652 0.355299652 0.355299652
> Fe1  0.144700378 0.144700363 0.144700378
> Fe1  0.644700468 0.644700408 0.644700408
> Fe  0.855299592 0.855299652 0.855299592
> O  0.555843592 0.944156408 0.24940
> O  0.24970 0.555843532 0.944156349
> O  0.944156468 0.24881 0.555843532
> O  0.444156408 0.055843621 0.74881
> O  0.75000 0.444156408 0.055843621
> O  0.055843592 0.74940 0.444156379
>
> which includes the second frame but also the first. Now if I type var
> xyzCoord = {1.3}.label(" %16.9[xyz]"); print xyzCoord
> I get 1, 2 and 3 and so on .
>  
>



-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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] how export in fractional coordinates

[P . Canepa]

Dear all, 

How can I export the fractional coordinates of one specif frame having loaded 
in Jmol a structure with several model? 
I am asking that question because I experienced the following drawbacks: 


Ok if I type var xyzCoord = {1.1}.label(" %16.9[xyz]"); print xyzCoord  i get 


Fe  0.355299979 0.35539 0.35539
Fe1  0.144699976 0.14461 0.14461
Fe1  0.644700050 0.644700050 0.644700050
Fe  0.85539 0.855300069 0.855300069
O  0.555899978 0.944100022 0.25030
O  0.24970 0.555899978 0.944100022
O  0.944100022 0.25060 0.555900037
O  0.444100022 0.055900037 0.75060
O  0.75000 0.444100022 0.055900037
O  0.055899978 0.75000 0.44403

When I do like var xyzCoord = {1.2}.label(" %16.9[xyz]"); print xyzCoord  i get 

Fe  0.355299979 0.35539 0.35539
Fe1  0.144699976 0.14461 0.14461
Fe1  0.644700050 0.644700050 0.644700050
Fe  0.85539 0.855300069 0.855300069
O  0.555899978 0.944100022 0.25030
O  0.24970 0.555899978 0.944100022
O  0.944100022 0.25060 0.555900037
O  0.444100022 0.055900037 0.75060
O  0.75000 0.444100022 0.055900037
O  0.055899978 0.75000 0.44403
Fe  0.355299652 0.355299652 0.355299652
Fe1  0.144700378 0.144700363 0.144700378
Fe1  0.644700468 0.644700408 0.644700408
Fe  0.855299592 0.855299652 0.855299592
O  0.555843592 0.944156408 0.24940
O  0.24970 0.555843532 0.944156349
O  0.944156468 0.24881 0.555843532
O  0.444156408 0.055843621 0.74881
O  0.75000 0.444156408 0.055843621
O  0.055843592 0.74940 0.444156379

which includes the second frame but also the first. Now if I type var xyzCoord 
= {1.3}.label(" %16.9[xyz]"); print xyzCoord
I get 1, 2 and 3 and so on . 

How can I make jmol printing just the coordinates which belongs to the second 
frame or the third when i type  {1.2}.label(" %16.9[xyz]") or  {1.3}.label(" 
%16.9[xyz]")? 


2) I cannot find in the script guide how to get the number of atoms of a 
certain frame. For instance I have a MgO cell with 4Mg and 4O atoms how can I 
know that the structure has 4 Mg and 4O? 

Thanks, Piero. 
--
Please consider the environment before printing this e-mail.

Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom

e-mail: pc...@kent.ac.uk
mobile: +44 (0) 7772-9756456
---


From: Robert Hanson [hans...@stolaf.edu]
Sent: Thursday, September 02, 2010 6:40 AM
To: P.Canepa
Subject: Re: how export in fractional coordinates

Piero, let's work on communicating more clearly.

I can't process little tiny messages like that. If you are still having 
problems with not being able to separate the two models, you need to send me 
the file (again if necessary -- no attachments in any of these messages in this 
thread) and explain exactly what you are having a problem with and what you are 
expecting to accomplish.

It sounds like you are developing some interesting things, and I'm happy to 
help you, but this particular thread is not working.

The best thing to do is to send me .jmol files that you create using

write .jmol

and then tell me exactly what commands you are having trouble with.

Also, for things like this that are simply "how do you use Jmol" questions, I 
would appreciate it if you would address those to 
jmol-users@lists.sourceforge.net, not 
hans...@stolaf.edu. That way others can help you at 
least as well as I can, and in the process more people will learn.

Thanks,

 Bob


On Wed, Sep 1, 2010 at 8:22 AM, P.Canepa 
mailto:pc...@kent.ac.uk>> wrote:
there it is
--
Please consider the environment before printing this e-mail.

Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom

e-mail: pc...@kent.ac.uk
mobile: +44 (0) 7772-9756456
---

From: Robert Hanson [hans...@stolaf.edu]
Sent: Wednesday, September 01, 2010 2:08 PM
To: P.Canepa
Subject: Re: how export in fractional coordinates

On Wed, Sep 1, 2010 at 7:32 AM, P.Canepa 
mailto:pc...@kent.ac.uk>>>
 wrote:
Please consider the environment before printing this e-mail.

Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
Un

Re: [Jmol-users] Find SMILES problem

[Otis Rothenberger]

 Bob,

Thanks. Your explanation of what aromatic means is the key here. I see 
now why this is happening. If I start with benzene and make 
1,3-cyclohexadiene, then it ends up in flat energy minimum that 
"minimize" does not change. I always get the lower case smiles. If I use 
"drag" to pull it out of shape, then I get upper case. If I make 
cyclohexene from benzene, "minimize" eventually get it and twists a bit. 
Once it twists, I get upper case.


One thing here is that it looks like the statement "aromatic just means 
flat and all sp2 for Jmol" is not quite correct. Flat seems to be a 
sufficient condition.


The context here may seem strange, but we are working on student model 
kit exercises, and we want the Jmol model kit to allow the same kind on 
tactile playing that a ball and stick model kit allows - e.g. take a 
double bond out of benzene. To be sure, I do not see the problem if I 
make 1,3-cyclohexadiene from cyclohexane. That should have been a clue 
that the flatness was the issue!


Re NIH, for all of the following, the Resolver returns benzene (no 
explicit hydrogens in submitted SMILES):


Jmol lower case benzene
Jmol lowercase cyclohexadiene
Jmol lower case cylohexene
Jmol lower case cyclohexane, which is, of course synonymous with 
"aromatic SMILES" for benzene.


Evidently, the Resolver is just ignoring "=" in this lower case context.

Otis

Otis Rothenberger
chemagic.com


On 9/2/2010 1:52 AM, Robert Hanson wrote:



On Wed, Sep 1, 2010 at 10:21 PM, Otis Rothenberger 
mailto:osrot...@chemagic.com>> wrote:


 Bob,

There is a general aromatic problem that I'm having with find SMILES
that's easiest to explain with a specific scenario. If I load benzene
and run "var x={*}.find('SMILES');echo @x," I get:

c1=cc=cc=c1

If I use model kit mode to make 1,3-cyclohexadiene, the same "var
x={*}.find('SMILES');echo @x" produces

c1=cc=ccc1


I'll look into that. Almost certainly a bug. It should only use lower 
case c if the ring is totally flat and there are no sp3 centers. I'm 
really surprised it's doing that. The code is only supposed to insert 
lower case "c" when:


-- the ring is flat
-- the ring has no sp3 centers

Is it possible you are sending it a flat no-hydrogen ring? When I use 
the model kit, I get:



C1==C1


I'm now stuck in lower case "c" mode on this ring no matter what I
do to
the ring. If I break a ring bond while the ring is no longer aromatic
and reform the bond, I go back to upper case "C"


remember -- "aromatic" just means "flat and all sp2" for Jmol. We're 
not going to get into multiple bonding issues. There's no 
"antiaromatic" here. It doesn't matter if you have 6 carbons and all 
single bonds or 6 carbons and all double bonds or 8 carbons (as in 
octadienyl dianion ligand). As long as it's flat and there aren't any 
tetrahedrally directed substituents, Jmol is going to use "c" instead 
of "C".


Bob


There are really two issues here:

1) Jmol creates Kekule SMILES in lower case, and this does not seem to
be standard. As long as compare is Jmol/Jmol, this is not a
problem. And
in fact, NIH Resolver which uses aromatic SMILES (c1c1),
recognizes
the Jmol lower case Kekule SMILES for benzene.


It's definitely incorrect. You really have all the H atoms there and 
it's not planar?


2) Getting stuck in lower case mode, however, is a problem and
seems to
be a bug.

I have a feeling that calculate/reset aromatic may offer one
solution to
the problem, but I'm not sure it can be used in a general sense to
"unaromatise" an aromatic ring. If this is not a bug, an
alternative is
to use JavaScript toUpperCase() on s, c, n, and o, but that has ugly
side affects.


See if you can find out more about what exactly the NIH server is 
requiring, if that's the issue. There's also a


/noaromatic/ flag in Jmol's SMILES business that turns off aromatic 
checking. That might be useful.


Help me define what the context is. Where are these being used?


Otis

--
Otis Rothenberger
chemagic.com 





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Re: [Jmol-users] [Jmol-developers] feature request: complexer hybrid orbitals

[Robert Hanson]

Look in new.htm -- there's a set of examples there.

On Thu, Sep 2, 2010 at 2:59 AM, Egon Willighagen  wrote:

> On Wed, Sep 1, 2010 at 11:05 PM, Robert Hanson  wrote:
> > done. I retro-added it to 12.0, just because.
> > Jmol 12.1.9 and 12.0.11 will have sp3d and sp3d2 hybridizations. See
> > documentation for details.
>
> Yeah, I saw it in the changelog yesterday! Cool!
>
> I will blog about this asap... the biggest problem here is to create a
> simple example smallest molecule with those hybridizations :)
>
> Many, many thanx!
>
> Egon
>
>
> --
> Dr E.L. Willighagen
> Post-doc @ Uppsala University (only until 2010-09-30)
> Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
> Homepage: http://egonw.github.com/
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
>
>
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>
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>



-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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] please test

[Robert Hanson]

Frieda, I've found a couple of bugs and have asked Nico to release 12.1.9
and 12.0.11. Let's see if those work for you and go from there.

Bob


On Thu, Sep 2, 2010 at 7:56 AM, Robert Hanson  wrote:

> Thanks, Frieda. I'm not seeing any "holes" (and because of a different
> discussion about a completely different kind of isosurface "hole" I'm not
> sure I know what you are referring to). Fill me in! [:)]
>
> There are a couple of bugs I uncovered in 12.1 -- looks like mapping with
> user color schemes isn't working properly, so I'll look into that. (I just
> see a complete but white isosurface)
>
> Bob
>
>
>
> On Thu, Sep 2, 2010 at 7:01 AM, Frieda Reichsman wrote:
>
>>
>> On Aug 31, 2010, at 7:41 PM, Robert Hanson wrote:
>>
>> > I would appreciate those recently requesting bug fixes to take a
>> > look at this version prior to our releasing it. The changes I made
>> > were rather involved, and I'm not sure I have all the files here to
>> > test it. I would appreciate your testing both 12.1.9 and 12.0.11
>> > (and especially 12.0.11).
>> >
>> > Frieda:
>> >
>> > # bug fix: isosurface "t.jvxl" map property temperature nonfunctional
>>
>> Hi Bob, Both versions of Jmol leave holes in the isosurface and do not
>> map the color to the surface when I have selected the correct set of
>> atoms prior to applying the surface. This is different from the
>> previous bug - and worse, I'm afraid. I'll send the files to you
>> offline.
>>
>> Frieda
>>
>>
>> -
>>
>> Frieda Reichsman, PhD
>> Senior Research Scientist
>> The Concord Consortium
>> http://concord.org
>> 25 Love Lane
>> Concord, MA 01742
>>
>> Office: 978-405-3228
>> Mobile: 413-320-7449
>>
>> Realizing the educational potential of technology.
>>
>>
>>
>>
>>
>>
>> --
>> This SF.net Dev2Dev email is sponsored by:
>>
>> Show off your parallel programming skills.
>> Enter the Intel(R) Threading Challenge 2010.
>> http://p.sf.net/sfu/intel-thread-sfd
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>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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] odd results (12.0.11 and 12.1.9)

[Pshemak Maslak]

  A case of odd outcome.

I have run the following in 12.0.11 and 12.1.9 (and compared to 12.0,8 
which I happen to have on my website)::

   isosurface cutoff 0.09 resolution 5 phase color  
translucent 7 atomicOrbital 2 0 0 1.0

One would expect three concentric isosurface spheres, the big "outside" 
one (red) and two small "inner" ones with the bigger of the two also red 
and the smallest blue; with all partially translucent.

That is indeed what is observed for 12.0.8, 12.011 and 12.1.9.

However rotation of the object leads to partial (12.0.11) or almost 
complete (12.1.9) "occlusion" of the most inner sphere as if the middle 
sphere had lost transparency of one of its halves.

It is difficult to describe, but clearly visible if the above script is 
executed in all three Jmol versions, side by side.

Not a big issue, but

PM

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Re: [Jmol-users] please test

[Robert Hanson]

Thanks, Frieda. I'm not seeing any "holes" (and because of a different
discussion about a completely different kind of isosurface "hole" I'm not
sure I know what you are referring to). Fill me in! [:)]

There are a couple of bugs I uncovered in 12.1 -- looks like mapping with
user color schemes isn't working properly, so I'll look into that. (I just
see a complete but white isosurface)

Bob


On Thu, Sep 2, 2010 at 7:01 AM, Frieda Reichsman  wrote:

>
> On Aug 31, 2010, at 7:41 PM, Robert Hanson wrote:
>
> > I would appreciate those recently requesting bug fixes to take a
> > look at this version prior to our releasing it. The changes I made
> > were rather involved, and I'm not sure I have all the files here to
> > test it. I would appreciate your testing both 12.1.9 and 12.0.11
> > (and especially 12.0.11).
> >
> > Frieda:
> >
> > # bug fix: isosurface "t.jvxl" map property temperature nonfunctional
>
> Hi Bob, Both versions of Jmol leave holes in the isosurface and do not
> map the color to the surface when I have selected the correct set of
> atoms prior to applying the surface. This is different from the
> previous bug - and worse, I'm afraid. I'll send the files to you
> offline.
>
> Frieda
>
>
> -
>
> Frieda Reichsman, PhD
> Senior Research Scientist
> The Concord Consortium
> http://concord.org
> 25 Love Lane
> Concord, MA 01742
>
> Office: 978-405-3228
> Mobile: 413-320-7449
>
> Realizing the educational potential of technology.
>
>
>
>
>
>
> --
> This SF.net Dev2Dev email is sponsored by:
>
> Show off your parallel programming skills.
> Enter the Intel(R) Threading Challenge 2010.
> http://p.sf.net/sfu/intel-thread-sfd
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> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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] please test

[Frieda Reichsman]

On Aug 31, 2010, at 7:41 PM, Robert Hanson wrote:

> I would appreciate those recently requesting bug fixes to take a  
> look at this version prior to our releasing it. The changes I made  
> were rather involved, and I'm not sure I have all the files here to  
> test it. I would appreciate your testing both 12.1.9 and 12.0.11  
> (and especially 12.0.11).
>
> Frieda:
>
> # bug fix: isosurface "t.jvxl" map property temperature nonfunctional

Hi Bob, Both versions of Jmol leave holes in the isosurface and do not  
map the color to the surface when I have selected the correct set of  
atoms prior to applying the surface. This is different from the  
previous bug - and worse, I'm afraid. I'll send the files to you  
offline.

Frieda


-

Frieda Reichsman, PhD
Senior Research Scientist
The Concord Consortium
http://concord.org
25 Love Lane
Concord, MA 01742

Office: 978-405-3228
Mobile: 413-320-7449

Realizing the educational potential of technology.





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Re: [Jmol-users] [Jmol-developers] feature request: complexer hybrid orbitals

[Egon Willighagen]

On Wed, Sep 1, 2010 at 11:05 PM, Robert Hanson  wrote:
> done. I retro-added it to 12.0, just because.
> Jmol 12.1.9 and 12.0.11 will have sp3d and sp3d2 hybridizations. See
> documentation for details.

Yeah, I saw it in the changelog yesterday! Cool!

I will blog about this asap... the biggest problem here is to create a
simple example smallest molecule with those hybridizations :)

Many, many thanx!

Egon


-- 
Dr E.L. Willighagen
Post-doc @ Uppsala University (only until 2010-09-30)
Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

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