Re: [Jmol-users] Displaying polymer chains with Jmol

2009-05-26 Thread Nick Greeves
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

[Jmol-users] Displaying polymer chains with Jmol

2009-05-26 Thread Nick Greeves
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

Re: [Jmol-users] jmol freezes

2009-04-24 Thread Nick Greeves
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

[Jmol-users] Safari error

2009-03-25 Thread Nick Greeves
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

[Jmol-users] Draw double-headed arrows?

2009-03-17 Thread Nick Greeves
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

Re: [Jmol-users] good idea?

2009-02-06 Thread Nick Greeves
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

[Jmol-users] jmol movie

2008-10-05 Thread Nick Greeves
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:

Re: [Jmol-users] Jmol-users Digest, Vol 29, Issue 5

2008-10-03 Thread Nick Greeves
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:

[Jmol-users] problem reading spardir file

2008-10-02 Thread Nick Greeves
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

Re: [Jmol-users] Jmol app - size of start-up window

2008-09-12 Thread Nick Greeves
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

[Jmol-users] Intermittent loading error

2008-09-09 Thread Nick Greeves
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

Re: [Jmol-users] javascript command fails in Safari?

2008-09-06 Thread Nick Greeves
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

[Jmol-users] New browser Chrome from Google

2008-09-02 Thread Nick Greeves
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

[Jmol-users] Mousewheel on Mac OS update

2008-09-01 Thread Nick Greeves
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

[Jmol-users] Issues with Polyhedra and cavities in solid structures

2008-08-13 Thread Nick Greeves
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

[Jmol-users] Save/load state command

2008-07-16 Thread Nick Greeves
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

[Jmol-users] Save/load state command

2008-07-15 Thread Nick Greeves
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.

[Jmol-users] Save/load state command

2008-07-14 Thread Nick Greeves
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

[Jmol-users] labels on multiple lines?

2008-06-27 Thread Nick Greeves
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

[Jmol-users] DRAW Charges on atoms + and - in animations

2008-06-08 Thread Nick Greeves
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

[Jmol-users] DRAW Charges on atoms + and -

2008-06-03 Thread Nick Greeves
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

[Jmol-users] Image Maps in Jmol wiki

2008-05-13 Thread Nick Greeves
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 [

Re: [Jmol-users] Image Maps in Jmol wiki

2008-05-13 Thread Nick Greeves
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

[Jmol-users] Image Maps in Jmol wiki

2008-05-09 Thread Nick Greeves
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

[Jmol-users] SMOL Files

2008-05-05 Thread Nick Greeves
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

[Jmol-users] Windows/Firefox Problem DNS is the key - SOLVED

2008-04-26 Thread Nick Greeves
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,

[Jmol-users] Windows/Firefox Problem DNS is the key ?

2008-04-24 Thread Nick Greeves
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

[Jmol-users] Automatic generation of multiple bond types

2008-04-03 Thread Nick Greeves
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.

[Jmol-users] Automatic generation of multiple bond types

2008-04-02 Thread Nick Greeves
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'

[Jmol-users] Conformational change and energy plot

2008-03-31 Thread Nick Greeves
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

[Jmol-users] Jmol applet export image

2008-02-17 Thread Nick Greeves
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

Re: [Jmol-users] What's new for Jmol

2008-02-17 Thread Nick Greeves
-- 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

[Jmol-users] What's new for Jmol

2008-02-15 Thread Nick Greeves
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

Re: [Jmol-users] Interactive 3D Organic Reaction Mechanisms

2008-01-04 Thread Nick Greeves
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

[Jmol-users] Interactive 3D Organic Reaction Mechanisms

2008-01-02 Thread Nick Greeves
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

[Jmol-users] No crash on Mac OS Leopard

2007-12-09 Thread Nick Greeves
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

[Jmol-users] Antialiasing looks good to me

2007-10-26 Thread Nick Greeves
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

[Jmol-users] New Resizable Window - Success

2007-10-19 Thread Nick Greeves
"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

[Jmol-users] new resizable Window

2007-10-19 Thread Nick Greeves
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

[Jmol-users] new resizable Window

2007-10-18 Thread Nick Greeves
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

[Jmol-users] Default Jmol menus - suggestion

2007-10-15 Thread Nick Greeves
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

[Jmol-users] bondOrder - what about 2.5 ?

2007-10-03 Thread Nick Greeves
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:

[Jmol-users] Back to teaching

2007-09-02 Thread Nick Greeves
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

[Jmol-users] Spin fps popup menu bug?

2007-07-11 Thread Nick Greeves
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

[Jmol-users] Access problems with Jmol content

2007-06-29 Thread Nick Greeves
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

[Jmol-users] Access problems with Jmol content

2007-06-28 Thread Nick Greeves
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

[Jmol-users] Not all chemicals are molecules

2007-06-08 Thread Nick Greeves
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

Re: [Jmol-users] Drawing arrows

2007-05-30 Thread Nick Greeves
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

[Jmol-users] Animation Help

2007-04-01 Thread Nick Greeves
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

[Jmol-users] New Window with resizable applet command?

2007-03-08 Thread Nick Greeves
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

[Jmol-users] New Window with resizable applet command?

2007-03-06 Thread Nick Greeves
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.

[Jmol-users] Colouring/highlighting bonds

2007-03-01 Thread Nick Greeves
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

[Jmol-users] Dynamic measurements

2007-02-16 Thread Nick Greeves
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

[Jmol-users] bonds between desired atoms - use CONNECT

2006-11-19 Thread Nick Greeves
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

[Jmol-users] Multiple Jmol panes - controlled by buttons?

2006-11-12 Thread Nick Greeves
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

[Jmol-users] Problem with JVXL data on Mac OSX - solution

2006-10-05 Thread Nick Greeves
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

[Jmol-users] Cube files and creating JVXL files

2006-08-18 Thread Nick Greeves
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

[Jmol-users] 3D Curly Arrows!

2006-08-16 Thread Nick Greeves
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.

[Jmol-users] Spartan PC .spartan reader implemented

2006-07-13 Thread Nick Greeves
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   

[Jmol-users] indexed isosurface and reading/writing JVXL files prototype

2006-05-26 Thread Nick Greeves
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

[Jmol-users] Safari crash with console open first

2006-05-04 Thread Nick Greeves
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

[Jmol-users] [ 1164344 ] Support for Spartan04 .smol vibration files (Open Babel)

2006-04-06 Thread Nick Greeves
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

[Jmol-users] New test pages

2006-04-05 Thread Nick Greeves
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

[Jmol-users] [ 1365894 ] Add isosurface commands to PopUp Menu?

2005-12-17 Thread Nick Greeves
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

[Jmol-users] Object fixes Mac problem (maybe)

2005-09-21 Thread Nick Greeves
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

[Jmol-users] Problem with Bob Hanson's Documentation and Mac Browsers

2005-09-03 Thread Nick Greeves
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

[Jmol-users] Jmol prerelease version 10.00.18 - Jmol.jar

2005-07-17 Thread Nick Greeves
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

[Jmol-users] Sarafi 10.4 Jmol problem confirmed

2005-05-07 Thread Nick Greeves
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:  

[Jmol-users] Safari 10.4 Jmol problem - absent

2005-05-07 Thread Nick Greeves
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

[Jmol-users] Jmol Bond Tolerance

2005-04-27 Thread Nick Greeves
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

[Jmol-users] (no subject)

2005-04-19 Thread Nick Greeves
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

[Jmol-users] Mac OS 10.3.9 fine here with Jmol (and everything else)

2005-04-17 Thread Nick Greeves
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

[Jmol-users] Help on vibrations - Spartan?

2005-03-16 Thread Nick Greeves
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

[Jmol-users] OS X 10.4 compatibility

2005-02-19 Thread Nick Greeves
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

[Jmol-users] JMol and Tiger OS X 10.4

2005-02-18 Thread Nick Greeves
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

[Jmol-users] m-xyz files "FOR REACTION COORDINATE"?

2005-01-19 Thread Nick Greeves
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