terms POLYMER and MONOMER are defined in relation to that. To
test, just
take any random PDB file and completely change the atom types to see
what
happens.
On Tue, May 26, 2009 at 4:49 PM, Nick Greeves >wrote:
Dear All,I am trying to find way of using Jmol to display non-
biological
po
Dear All,
I am trying to find way of using Jmol to display non-biological
polymers e.g. polystyrene, nylon, bisphenol A and to highlight the
monomer units within the chain.
I have found the commands POLYMER, MONOMER, and SUBSTRUCTURE which
look as though they should be useful but I have bee
I tried but it would not freeze for me. I haven't experienced this
before.
Safari 4 beta, 10.5.6 Mac Pro 4 Gb RAM
java -version
java version "1.5.0_16"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_16-
b06-284)
Java HotSpot(TM) Client VM (build 1.5.0_16-133, mixed mode, sharing
I had an unfortunate experience today while using Safari 4.0 beta
(5528.16) on Mac OS 10.5.6 to display some local web pages in a
lecture. I have done this many times before.
Safari showed a red X in the top left hand corner of the Jmol window
(I don't recall seeing this in Safari before bu
Dear All,
We have used drawing arrows http://chemapps.stolaf.edu/jmol/docs/examples-11/draw.htm
to create 3D curly arrows for organic reaction mechanisms for some
time.
We would like to be able to create 3D double headed arrows e.g. for
the shorthand mechanism of reactions of acid derivative
Hi Bob et al,
It is very clever and works nicely.
I'm not sure about it being default behaviour though I think it would
be confusing for new/occasional users. And for us it is less flexible
than the Console as you can't paste (or I couldn't, Safari) or copy
once a command does the desired th
Fine on MacOS X 10.5.5/Safari/QT resolution clear but rather fast to
actually see anything!
While it was downloading, it played a bit then stopped and was
pixelated. Fine once it was all downloaded though.
All the best
Nick
--
3D Organic Animations http://www.chemtube3d.com
Tel:
Hi Dean,
Something like this? http://www.chemtube3d.com/BenzeneMOs.html
I use connect 2 (carbon) (carbon) AROMATIC;
All the best
Nick
--
3D Organic Animations http://www.chemtube3d.com
Tel: +44 (0)151-794-3506 (3500 secretary)
On 3 Oct 2008, at 00:06, [EMAIL PROTECTED] wrote:
Hi Jeff,
I have seen that sort of error when the Spartan file is open and you
try and read it with Jmol.
If you are using a Mac you can hold down option-alt while Exporting
and select Jmol format for a multiple .xyz file. That is what i use.
All the best
Nick
--
3D Organic Animations htt
Message: 2
Date: Fri, 12 Sep 2008 15:32:59 -0500
From: "Robert Hanson" <[EMAIL PROTECTED]>
Subject: Re: [Jmol-users] Jmol app - size of start-up window
To: jmol-users@lists.sourceforge.net
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
Someone more familiar
Hi Steve,
I've also had complaints from IE users (particularly) about this with
my site. Today I managed to duplicate the problem and capture the log
with IE7/XP.
FileManager.openFile(test/advanced/ReO3.cif) //test/advanced/ReO3.cif
FileManager opening http://www.chemtube3d.com/solidstate/te
No problems on Safari here.
On 6 Sep 2008, at 16:58, [EMAIL PROTECTED] wrote:
If anyone else observes this intermittant failure of Jmol's
javascript command in Safari, I suggest that this be mentioned as a
caution in the Jmol documentation entry on javascript.
My OS X and Safari are up to dat
Just to save anyone else the pain of getting Jmol working with
Google's new browser Chrome http://www.google.com/chrome/
You need a pre-release version of Java http://java.sun.com/javase/downloads/ea.jsp
then it works (so far).
All the best
Nick
--
3D Organic Animations http://www.chemtube
A while ago I raised the question of whether Jmol could be adapted so
that Mac users could use their mouse wheel (or two fingers on the
trackpad) to zoom in Jmol as happens in IE/Windows.
At that time there was a problem with Safari/Java not recognising the
MouseWheel events but I am pleased
Hi All,We have been trying to use Jmol to display coordination polyhedra for a range of inorganic structures and have encountered what seems to us anomalous behaviour. I have set up some of the pages on an external server using Jmol 11.6RC6 so that anyone interested can take a look. These pages are
Good point Angel,
The load command also shows different behaviour on a website (Bob's)
or in Dreamweaver.
Web: load /*file*/"http://chemapps.stolaf.edu/jmol/docs/examples-11/data/quartz.cif
" {1.0 1.0 1.0};
DW: load /*file*/"file:/Volumes/nggroup/external/test/histidine.cif";
(this is on Mac
t
Nick
--
3D Organic Animations http://www.chemtube3d.com
Tel: +44 (0)151-794-3506 (3500 secretary)
4. Save/load state command (Nick Greeves)
5. Re: Save/load state command ( Angel Herr?ez )
9.
Is it possible to save a state and then reload that state from disk or
as part of a very long command?
save state, move molecule, restore state works just fine but I'd like
to be able to load such a state from scratch without having saved it
in the same session.
All the best
Nick
--
3D Orga
Hi All,
A simple query about the label command.
Is it possible to force labels onto two or more lines so that parts of
the label appear above one another?
e.g.
C
3
rather than
C3
All the best
Nick
--
3D Organic Animations http://www.chemtube3d.com
Tel: +44 (0)151-794-3506 (35
Hi Angel, Bob, et al,
I think we've cracked the problem of centering charges, lone pairs,
radicals etc. on atoms in animations.
http://www.chemtube3d.com/sandbox/Carbenes2.html shows an example. I
recommend the "larger view" to see the details.
select all;set labelOffset 0 0;font label 20 se
Hi Angel,
A very timely contribution. I was looking for a way to show positive
and negative charges on atoms.
A few experiments later I find that
draw {atomno=4} "+"
draw {atomno=4} "–"
works quite nicely.
Control over the colour and font size would be great and Bob suggested
that Unicode
ks, then use instead:
_jmol.noEval = true;
just prior to the jmolApplet command. This options was designed
specifically with wikis in mind.
Great planning!
Also...
Nick Greeves wrote:
>
> The next issue was the path to the file to be loaded - this works.
>
> rect 3 14 103 96 [
Hi Paul,
Many thanks for your suggestions.
After major assistance from Bob Hanson and much trial and error, I now
have Image Maps working in my wiki sandbox
http://osxs.ch.liv.ac.uk/~ng/wiki/index.php/Test_area3 - not all the
maps areas are in place. I also note that the applet resizes with t
This might be regarded as off topic, but I hope someone here reads PHP.
I'm trying to get image maps to execute Jmol commands inside a
MediaWiki using Nico's Jmol extension.
Jmol windows are loading just fine but I need to pass the commands
from the image maps. I contacted Tim Starling who w
Hi Otis,
.smol files are found inside the package of standard MacSpartan 04
files which is terminated .slst Use the Show Package contents menu
option. You can export from Spartan 06 as MacSpartan 04 and that will
have the .smol file inside.
However thanks to Bob's earlier efforts, there is a
Thanks to all who replied especially Rolf and Eric. This is a
situation where your IT department is your friend.
I spoke to CSD in Liverpool and were able to set the forward and
reverse lookups for the server IP address so that ChemTube3D is back
for non-Mac Firefox users ;-)
Date: Thu,
My site has been bitten by this recent
java.security.AccessControlException problem. It seems only to be FF/
Win users who suffer.
Click on the bottom left structure in the reaction scheme once the
page has loaded. You should see a new structure in the Jmol window.
I'm using image maps to
s
To: jmol-users@lists.sourceforge.net
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Nick Greeves wrote:
Is there a command which will generate multiple bond types (even just
double would be a start) from a structure that lacks such info e.g.
Is there a command which will generate multiple bond types (even just
double would be a start) from a structure that lacks such info
e.g. .xyz ?
I've looked at Connect Calculate and Set autobond ON but none seem to
do the job.
connect aromatic auto does the job for aromatic compounds but I'
Hi Bob et al,
This looks very interesting.
Could the energy plot for rotation of a methyl group be extended to
show an interactive energy graph for any change in conformation? In
the past I have used QuickTime movies from Spartan to display this but
it would be much nicer to use Jmol.
e.g. S
Hi Angel,
Works on Safari, Firefox, Camino on Mac OS X 10.5.2
I'll try and set it up on my server which already runs PHP.
Looks great from here!
All the best
Nick
--
3D Organic Animations http://www.chemtube3d.com
Tel: +44 (0)151-794-3506 (3500 secretary)
On 17 Feb 2008, at 2
--
3D Organic Animations http://www.chemtube3d.com
Tel: +44 (0)151-794-3506 (3500 secretary)
On 16 Feb 2008, at 23:17, Eric Martz wrote:
At 2/15/08, Nick Greeves wrote:
3D curly arrows for organic reaction mechanisms - Henry Rzepa said
nothing else can do this.
Display of
Hi Bob,
You've got any easy job, so much great new stuff! The problem is to
pick the "best"!
I'd be pleased if you chose to highlight any of the examples from
ChemTube3D.com which are all beneficiaries of recent developments.
I'll try and assist by picking out some of my favourites:
3D c
Hi Henry,
Thanks for your kind comments. I see what you mean about the
"antarafacial" nature of the ozonolysis. I had not intended to imply
any antara/suprafacial aspect to the 3D arrows but like you I think
this could be used specifically to stress this important aspect
perhaps by using a
would be very grateful for any feedback, suggestions for important
new reactions that should be included would be welcome, as would
corrections and comments.
Best regards
Nick
--
Nick Greeves MA Ph.D. via OS X Mail
Senior Lecturer in Organic Chemistry
Department of Chemistry
Fine here, Safari and Firefox/OS X 10.5.1
All the best
Nick
--
WWW Pages: http://www.liv.ac.uk/Chemistrywww/Staff/greeves.html
Tel: +44 (0)151-794-3506 (3500 secretary)
On 9 Dec 2007, at 14:05, [EMAIL PROTECTED] wrote:
Question, are people seeing this problem at
http://chemap
Hi Bob,
I've tested the resizable window command with the new antialias
settings and the new version looks great.
How should this be controlled from the applet? (In the view popup
menu?) Should antialiasing be on by default? (gets my vote)
All the best
Nick
--
WWW Pages: http://www.liv.ac
"100%","90%"]
and then to collect a script from the opening page
El 19 Oct 2007 a las 16:27, Nick Greeves escribi?:
I'm still struggling with creating a button to pop out a large Jmol
window like you have below your windows as standard.
So, you can just
Hi Angel,
It is a feature of Bob's standard page http://chemapps.stolaf.edu/
jmol/docs/examples-11/new.htm just underneath the Jmol pane 'new
resizable window'.
It calls newAppletWindow() and works beautifully but NOT for my button.
I'm still struggling with creating a button to pop out a la
Hi Bob,
I'm still struggling with creating a button to pop out a large Jmol
window like you have below your windows as standard. Rolf's
suggestion creates a button on the page but it does nothing and gives
an error in Console.
(event handler):Can't find variable: newAppletWindow
I guess i
Hi All,
When Bob produced the ability to customise the menus I thought -
great ultimate power! Then I thought, users might be unsettled by
missing options etc. And site builders might forget they had
eliminated features!! So I still think the default set is probably key.
My query is: why i
Hi Bob et al,
I would like to request 2.5 is recognised as well and interpreted as
a double bond and a partial bond.
I have wished for this in acylium ion formation and reactions of
alkynes.
All the best
Nick
--
WWW Pages: http://www.liv.ac.uk/Chemistrywww/Staff/greeves.html
Tel:
Hi Bob,
As you can see from my signature I understand what you mean!
I have to say that the changes you have made to Jmol over the last
year or so have transformed it into a fantastically powerful and
versatile tool. Great job!
You may recall asked you for advise about how to get an undergradu
Hi Bob et al,
I think I have uncovered a problem with the popup menu in Jmol 11.3.2
as exemplified http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
Issuing the commands from the popup menu leads to errors in console
e.g. Set X rate 10
script ERROR: unrecognized SPIN = parameter: X
Thanks for your thoughts Bob.
The pages are very plain HTML, no XML in sight, but I was using a
very recent and newly acquired build of Safari 3(.02) so maybe that
was to blame. I did quit and restart the browser. I'll keep an eye on
this one.
What is odd is that the same pages are fine at
I observed odd behaviour with my Jmol pages when viewed from the
network of a local college today. Instead of Jmol performing as
expected I got a red cross in a small document icon top left of the
white rather than black Jmol window.
The network displayed the BBC website normally but none o
Hi All,
I saw this proposed change on the list and have now seen it on the
web site. Initially I let it slide but the more I think about it the
more I think I was wrong.
"Jmol - an open-source Java viewer for three-dimensional
chemical structures" - this is accurate.
Molecular structures is
I saved this from Bob Hanson last year as a nice way to draw and move
curves and arrows. It worked for me back then.
All the best
Nick
--
WWW Pages: http://www.liv.ac.uk/Chemistrywww/Staff/greeves.html
Tel: +44 (0)151-794-3506 (3500 secretary)
On 16 Aug 2006, at 14:39, [EMAIL
Hi Karl,
I use the Mac version of Spartan 04 to export collections of files as
multiple-xyz files. The option is semi-hidden. You have to hold down
option(Alt) while selecting Export to get the xyz(Jmol) option and I
don't know if the Windows version has this option (I requested it for
Mac
Thanks Rolf,
That works nicely.
I've noticed something else I don't understand. On Bob's page
http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new0.htm
if I enter javascript:newAppletWindow() into the cmd: window and
press return it basically works but I get a Javascript message
I agree this works well and made me think about how it could be used
more widely.
In ordinary web pages I often use the Open Link in New Window(Frame)
feature of my browser (Safari) to create a new window of the content
I want to scrutinise in more detail without losing the initial page.
Is there a way to select and hence color certain bonds blue or
whatever or to have some bonds wireframe 0.1 and some wireframe 0.2?
I'm particularly thinking of Newman projections where a difference is
needed between "front" and "back".
http://www.stolaf.edu/academics/chemapps/jmol/docs/ind
On 16 Feb 2007, at 06:31, <[EMAIL PROTECTED]>
<[EMAIL PROTECTED]> wrote:
DYNAMIC MEASUREMENTS
Now that we can move atoms so easily, we don't want those
measurements getting stale.
set dynamicMeasurements
allows measurements to be recalculated on the fly.
Hi Bob,
Two sugge
I had just this problem recently and all I needed was here
http://www.stolaf.edu/academics/chemapps/jmol/docs/?ver=11.0#connect
All the best
Nick
--
WWW Pages: http://www.liv.ac.uk/Chemistrywww/Staff/greeves.html
Tel: +44 (0)151-794-3506 (3500 secretary)
On 18 Nov 2006, at 2
how
it might be done?
(Bob, all your examples I could find had just one overworked Jmol pane!)
All the best
Nick
--
Dr Nick Greeves Webmaster via Entourage
Department of Chemistry
University of Liverpool
Donnan and Robert Robinson Laboratories
Crown Street, LIVERPOOL L69 7ZD U.K
Hi Frieda,You can drag and drop to and from the Console window as I've done here, or look in console.log using the Console.app application. You can copy from console.log.JVXL solvent-excluded surfacerange (-3.331551, -2.0765, -3.5629022) to (3.331551, 2.0765, 2.1107209)-10 -6.295719 -3.9240162 -6.7
Cube files are produced by Gaussian. You can also use Spartan files http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/isosurface.htmTo create a JVXL file, load a cube/smol etc. file, set Java Console Log level: to 5 and display the surface you require. Look in Console log for the outpu
Hi Bob,I have now seen your latest idea in action on XP/IE (rather than the errors on Mac OS X) so I can be enthusiastic rather than frustrated.We have 3-D curly arrows for organic mechanisms and I guess by scripting we can animate their arrival - nice! All the bestNick-- WWW Pages: http://www.
Looks good Bob.Any news of the equivalent Mac Spartan files?Minor problem on http://www.stolaf.edu/people/hansonr/jmol/test/proto/new.htmload "acetic acid.spartan"script ERROR: ScriptException:java.io.FileNotFoundException: http://www.stolaf.edu/people/hansonr/jmol/test/proto/acetic acid.spartan
Hi Bob,Just checked out indexed isosurface and reading/writing JVXL filesWorks like a charm on Safari/OS X 10.4.6Fantastic! I particularly enjoyed the CH3Cl electrostatic potential mapped on electron density.Now if only JMol could read Spartan files as well as .cube. All the bestNick-- WWW Pag
I can confirm the Safari crash. Truncated log below in case it helps. All the bestNick-- WWW Pages: http://www.liv.ac.uk/Chemistrywww/Staff/greeves.htmlTel: +44 (0)151-794-3506 (3500 secretary) On 4 May 2006, at 22:36, [EMAIL PROTECTED] wrote:SAFARI CRASHES Frieda Reichsman has obs
I'm keen to be able to use Spartan 04 files directly with Jmol. The latest version can open some of my .smol files but not all. To my mind http://jmol.sourceforge.net/demo/vibration/ is an excellent way of displaying all the various vibrations a molecule can undergo.The benzenevib.slst.zip file I u
Bob,These work as expected and make the new features very clear.My only comment is that I did not expect that connect DELETE AROMATIC would leave nothing between those atoms. Co3porph shows this clearly.Of course it makes sense but Organic chemists expect to see bonds of some sort! All the bestNic
Now seems a good time to draw attention to an enhancement request I filed a while ago.Add isosurface commands to PopUp Menu?The recent addition of support for .cube format files allows the display of surface such as molecular orbitals etc. which is very useful.http://www.stolaf.edu/people/hansonr/j
Hi Bob,Both of these pages work fine for me OS X 10.4.2 Safari 2.0.1 (412.5).The dreaded popups (which had problems) have gone?? Anyway, the new layout looks (and works) great! All the bestNick-- WWW Pages: http://www.liv.ac.uk/Chemistrywww/Staff/greeves.htmlTel: +44 (0)151-794-3506
Periodically I check out Bob's excellent documentation and I've noticed the demo popup windows don't work with Safari/Firefox/Netscape under Mac OS X 10.4.2.e.g. Safari 2.0.1 load http://www.stolaf.edu/people/hansonr/jmol/docs/#.stereoclick on Examples: in new window using 1crn.pdbwait for Jmol to
Has Jmol.jar been updated in the same way to handle these new features? All the best Nick -- WWW Pages: http://www.liv.ac.uk/Chemistry/Staff/greeves.html Tel: +44 (0)151-794-3506 (3500 secretary, 7886 voice mail)On 17 Jul 2005, at 04:24, [EMAIL PROTECTED] wrote:Jmol prerelease
Hi Phil,I misunderstood where I was supposed to click next and was choosing location 0 with and without callbacks (I knew Safari was weak with callbacks and thought this was the point).When I try a DIFFERENT location I see the problem.I'll file this bug as well. All the best Nick -- WWW Pages:
I cannot reproduce this error. OS X 10.4 Safari works for me. All the best Nick -- WWW Pages: http://www.liv.ac.uk/Chemistry/Staff/greeves.html Tel: +44 (0)151-794-3506 (3500 secretary, 7886 voice mail)On 7 May 2005, at 14:57, [EMAIL PROTECTED] wrote:Steps to Reproduce: Go to
Is it possible to change the default bond tolerance so that bonds are shown (or not) as required? In the Java app version of Jmol this is achieved by a slider but I don't know if the web based version can be controlled in this way.Perhaps a parameter with a value 0-1 Å as in the app??Jmol does use
From: Bob Hanson <[EMAIL PROTECTED]>To: jmol-users@lists.sourceforge.netSubject: [Jmol-users] power of jmol appletReply-To: jmol-users@lists.sourceforge.netI'll be interested if the following page works for you:http://www.stolaf.edu/people/hansonr/jmol/applet/mscalc/view.htmThis page demonstrates c
about problems with
Java. What are others observing -- before I take the plunge?
Phil
All the best
Nick
--
Dr Nick Greeves Webmaster via OS X Mail
Department of Chemistry
University of Liverpool
Donnan and Robert Robinson Laboratories
To my mind http://jmol.sourceforge.net/demo/vibration/ is an excellent way of displaying all the various vibrations a molecule can undergo.
But based on Bob Hansons recent comments on Gaussian file parsing I wonder if now is a good time to suggest that the vibration output from Spartan 04 should b
miserably in 10.3!) Fails (miserably) under Tiger too - details sent off list to Henry. All the best Nick -- Dr Nick Greeves Webmaster via OS X Mail Department of Chemistry University of Liverpool Donnan and Robert Robinson Laboratories
Henry et al,I'd be delighted to test any Jmol based pages with OS X 10.4.Please let me have the URLs and details of the OS/browser combination that produces ideal results.To date I can say that things are generally better with Safari than under Panther. All the Jmol home site is fine.All the bestNi
2.2065 1.1728
C0.0013 2.2193 1.1610
C -0.5553 0.8094 1.1544
snip
All the best
Nick
--
Dr Nick Greeves Webmaster via OS X Mail
Department of Chemistry
University of Liverpool
Donnan and Robert Robinson La
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