Re: [Jmol-users] Test2

@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- ___ Jmol-users mailing list Jmol-users

[Jmol-users] MacBook and iPad Note

the results locally before I move content to server. And I can do it all on an iPad with very little pain. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- ___ Jmol

[Jmol-users] Local Storage

Jmol/JME note book comes to mind immediately. Sorry if this is old hat, but like I said, this is all new and kind of wonderful to me. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com

Re: [Jmol-users] iFrame and Test Request

)); } else { $('#vmk2')[0].contentWindow.introEcho = echo; $('#vmk2')[0].contentWindow.loadModel(models2/ethane.txt); } }); -- Otis Rothenberger CheMagic.com On Jul 31

[Jmol-users] iFrame and Test Request

the former (Jmol script) - not the latter (JavaScript). Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- Infragistics Professional Build stunning WinForms apps today! Reboot your WinForms applications

Re: [Jmol-users] Survey Question re Run Jmol Locally

this. I was just interested in the various specific reasons. Thanks again for the response. Your answer to B is particularly helpful. Otis Rolf Huehne mailto:rhue...@fli-leibniz.de July 29, 2014 at 9:37 AM On 07/28/2014 04:55 PM, Otis Rothenberger wrote: I'm putting together a presentation, and I

[Jmol-users] Survey Question re Run Jmol Locally

of the picture. E) Other Thanks in advance for any replies... Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- Infragistics Professional Build stunning WinForms apps today! Reboot your WinForms

[Jmol-users] RCSB

. Constructing a test post search on the RCSB REST page also produces 0 matches. It anyone else seeing this problem. Otis -- Otis Rothenberger o...@chemagic.com -- ___ Jmol-users

Re: [Jmol-users] JMol PHP Recentl error with Firefox 30

://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger o...@chemagic.com -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https

Re: [Jmol-users] State Question

of error messages? I would use set debugscript first, then run that and see what it gives. Bob On Wed, Jul 9, 2014 at 10:58 PM, Otis Rothenberger osrot...@chemagic.com wrote: Bob, I use the following script to duplicate a model in the Jmol window: scpt = 'center;var mod2

[Jmol-users] State Question

. This is not a huge problem. I'm just curious if the renumbering is the guilty party. Otis -- Otis Rothenberger o...@chemagic.com -- Open source business process management suite built on Java and Eclipse Turn processes

Re: [Jmol-users] Drag/Drop

of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger o...@chemagic.com

Re: [Jmol-users] Drag/Drop

(); ev.preventDefault(); On Wed, Jul 2, 2014 at 11:39 AM, Otis Rothenberger osrot...@chemagic.com wrote: Bob, I don't think this one is a cache issue: On the latest version of JSmol, I can no longer drag/drop/load a model from a molfile. Otis -- Otis Rothenberger o...@chemagic.com

[Jmol-users] Drag/Drop

Bob, I don't think this one is a cache issue: On the latest version of JSmol, I can no longer drag/drop/load a model from a molfile. Otis -- Otis Rothenberger o...@chemagic.com -- Open source business process

Re: [Jmol-users] Jmol 14.2.1

. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr -- Otis Rothenberger o...@chemagic.com -- Open source business process management suite built on Java and Eclipse Turn processes into business

Re: [Jmol-users] Jmol 14.2.1

Bob, Ignore the previous note. The Chrome cache clearing add-on is evidently a piece of junk! When I went into preferences to clear cache, the problem disappeared. Otis On Sun, Jun 29, 2014 at 4:36 PM, Otis Rothenberger osrot...@chemagic.com wrote: Bob, Safari seems OK, but I'm seeing

Re: [Jmol-users] Disable crystal information

Angel and Herman, I think it's simply: set unitcell off Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Jun 16, 2014, at 2:46 PM, Angel Herráez angel.herr...@uah.es wrote: Then it must be a typo or a change When I enter in the console show showunit? (meaning

Re: [Jmol-users] Disable crystal information

Herman, There may be a more elegant way to do this, but the following should work: set unitcell off; draw unitcell MESH NOFILL The mesh nofill prevents the drawing of the solid unit cell. You may have to play with colors if you don't want the default. Otis -- Otis Rothenberger o

Re: [Jmol-users] Disable crystal information

Angel, Set unitcell off takes them both out, at least in JSmol - text and cell. Per my second note, set unitcell off; draw unitcell MESH NOFILL while not elegant should get the job done. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Jun 16, 2014, at 4:00 PM, Angel

Re: [Jmol-users] JSmol2wp version 0.7 beta

an authoritative answer. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Jun 11, 2014, at 10:08 AM, Robert Hanson hans...@stolaf.edu wrote: Should I just remove the difference and make InChIKey and InChI both standard? On Wed, Jun 11, 2014 at 8:56 AM, Otis Rothenberger osrot

Re: [Jmol-users] JSmol2wp version 0.7 beta

Bob, Very nice executive summary on the whole issue: http://www.inchi-trust.org/fileadmin/user_upload/html/inchifaq/inchi-faq.html#2.9 Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Jun 11, 2014, at 10:08 AM, Robert Hanson hans...@stolaf.edu wrote: Should I just

Re: [Jmol-users] Testing Help

Thanks Greg, This is very helpful, especially your ability to test #2. I need to get back to the ISU folks to let them know that this seems to be working. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Jun 9, 2014, at 4:44 AM, Greg.Black greg.bl...@open.ac.uk wrote

[Jmol-users] Testing Help

for any assistance. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases

Re: [Jmol-users] saving files from JSmol in Chrome - filename is lost

Angel, In Chrome preferences, there is a checkbox option under downloads: Ask where to save each file before downloading If this option is checked, you will be able to name a download file before saving. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On May 27, 2014, at 4

Re: [Jmol-users] tying echoes to sets of frames

Greg, If you go to chemagic.com and click the miscellaneous button, the animation links are at the bottom of the misc control screen. The frames file for this one is chemagic.com/animations/diels_alderF.TXT Individual frames are simply molfiles pulled from Jmol. At the time we did this, we

Re: [Jmol-users] tying echoes to sets of frames

bonds all around;delay 4;echo;} delay @{frameInterval}; } echo The final product is this substituted cyclohexene. ;delay 3;boundbox {*};centerat boundbox;zoom 0; -- Otis Rothenberger o...@chemagic.com http://chemagic.com On May 16, 2014, at 10:13 PM, Frieda Reichsman frieda...@mac.com wrote

Re: [Jmol-users] Jmol 14.1.15 released

Bob and Phil, I see the same thing. Bob, you're getting a 400 error because of an inadvertent space in your URL: http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound /name/acetone/SDF?record_type=3d Note the space after the word compound in your URL above. Otis -- Otis Rothenberger o

[Jmol-users] AtomNo AtomIndex Issue

the consequence of convolution? Perhaps I should just use atomno for my subsequent operations. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- Is your legacy SCM system holding you back? Join Perforce

[Jmol-users] Jmol.evaluate problem

); } After some really weird logic behavior, I finally took a look at this: alert(Jmol.evaluate(jmolApplet0, ' + key + '.find('SMILES',' + ans + ') 0) == false); With key and ans as different SMILES, the alert was true. 14.1.12_2014.03.21 Otis -- Otis Rothenberger o...@chemagic.com http

Re: [Jmol-users] Jmol.evaluate problem

Thanks Bob. It's right there in the docs all marked in green! I just missed it. -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Apr 21, 2014, at 6:31 PM, Robert Hanson hans...@stolaf.edu wrote: (Jmol.evaluate can only return String, Integer, or Float values, as was the case

Re: [Jmol-users] Jmol.setInfo

window, but again that info screen is so convenient. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Apr 15, 2014, at 1:07 PM, Robert Hanson hans...@stolaf.edu wrote: You mean what you see with jmolApplet._showInfo(true) ? Info.console=none will disable

[Jmol-users] Jmol.setInfo

Bob, Is there a way to turn off error reporting to the Jmol.setInfo screen? Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases

Re: [Jmol-users] Problem with Test2.htm CONFIRMATION

I'm running 14.1.12_2014.3.21 and it's OK Mac Safari, Chrome, and Firefox. This is OS 10.9.2 Mavericks. I've been keeping a close eye on iPad, and this version of JSmol runs really well on iPad Air and iPad 2. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Apr 13, 2014

[Jmol-users] Problem with Test2.htm

, it just disappears. Is anyone else seeing this? Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously

Re: [Jmol-users] Problem with Test2.htm

flashes on. Shortly after that a mouse movement makes the model disappear. I'm seeing it on iPad also. Again, it's random, so it's hard to test. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Apr 12, 2014, at 10:10 PM, Otis Rothenberger osrot...@chemagic.com wrote: Bob

[Jmol-users] Question re filetype

Bob, If I do var x= load filePath is there a quick way to determine the fileType of the file in x? I'm trying to make pre-load load script decisions. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com

Re: [Jmol-users] iPad Script Question

Thanks Bob. It's just that 2 looked weird to me. They both work on iPad and Android, so I'm a happy camper. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Apr 6, 2014, at 11:23 PM, Robert Hanson hans...@stolaf.edu wrote: looks great to me On Sat, Apr 5, 2014

[Jmol-users] iPad Script Question

hope on this several months ago. Android Chrome isn't too shabby either. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- ___ Jmol-users mailing list

Re: [Jmol-users] last chance before Jmol 14.1.11; JJSME/JSpecView

problem was evident there also. I think this was working earlier this week - server problems at some point along the route? Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Mar 21, 2014, at 6:08 PM, Pshemak Maslak n...@psu.edu wrote: On 3/6/2014 11:23 PM, Robert Hanson

Re: [Jmol-users] Problem with Firefox and PubChem download

domain issue. After your note, this may well work because I change the response type before I send it from the server - i.e. unrelated to cross domain. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Mar 7, 2014, at 12:42 PM, Robert Hanson hans...@stolaf.edu wrote: I could

Re: [Jmol-users] Problem with Firefox and PubChem download

with SMILES. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Mar 7, 2014, at 3:24 PM, Robert Hanson hans...@stolaf.edu wrote: Jmol handles this by POSTing the request, not GETting it: FileManager.getAtomSetCollectionFromFile(http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles

Re: [Jmol-users] Jmol speed

on a direct browser load. I get all this remote stuff through AJAX and chemagic server scripts, so I'm not sure how long this may have been an issue. Mac Chrome is fine, and the subsequent cholesterol MEP speed is good. Is anyone else seeing this PubChem issue with Safai? Otis -- Otis

Re: [Jmol-users] wrong state after calculate hydrogens

0.7347967540624076 - - - - 7 H -0.4272906203972308 -0.45489682342005144 -0.9058099170150967 - - - - 8 H -0.7788497796450441 -0.2519180940621916 0.7347994928080308 - - - - 9 end append inline;; Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Mar 1, 2014, at 7:15 AM, Angel Herráez

Re: [Jmol-users] ModelKit fix

with the multiple version listings in the console. Here's the two versions by my best interpretation: 14.0.10_2014.02.19 14.1.11_2014.02.22 Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Feb 24, 2014, at 9:14 AM, Ron Mignery remign...@gmail.com wrote: The problem I saw

Re: [Jmol-users] Jmol 14.1.11_2014.02.22

to use measure. I'll check this out again in the morning. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Feb 22, 2014, at 11:16 PM, Robert Hanson hans...@stolaf.edu wrote: ___JmolVersion=14.1.11_2014.02.22 http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.11_2014.02.22.zip

Re: [Jmol-users] ModelKit broken in 14.0.10

Ron, I may not have played with it enough yet, but I don't see it crashing here: http://chemistry.illinoisstate.edu/osrothen/JSmolVMK2.htm Native model kit menu and our model kit script control menu seem ok on Mac Safari and Chrome. I can't check Windows right now. Otis -- Otis Rothenberger

Re: [Jmol-users] Model Kit Bond Click

Bob, I forgot to put in the note last night that you still cannot close the model kit mode menu once it's opened. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Feb 17, 2014, at 2:20 AM, Otis Rothenberger osrot...@chemagic.com wrote: Bob, Our VMK page model edit

Re: [Jmol-users] Model Kit Bond Click - More Playing

a single box checked lead to uncertain actions. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Feb 17, 2014, at 7:38 AM, Otis Rothenberger osrot...@chemagic.com wrote: Bob, I forgot to put in the note last night that you still cannot close the model kit mode menu

[Jmol-users] Question

Bob, I hate to bug you while you're chasing bugs (ouch), but a quick question: I currently load only JSmol.min.js on page load. Is there any file or files that could be loaded to immediately cache model kit activity, specifically bond and atom change? Otis -- Otis Rothenberger o

Re: [Jmol-users] Model Kit Bond Click

. This appears to be a menu problem. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Feb 16, 2014, at 10:07 PM, Robert Hanson hans...@stolaf.edu wrote: Otis, could you try that again? With the release at SourceForge? This just replaces the file of the same released Friday

[Jmol-users] Model Kit Bond Click

window. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth

Re: [Jmol-users] Model Kit Bond Click

Sorry Bob. I was focusing on the NMR stuff, which I had on the ISU server. I had an older version of JSmol on the CheMagic server. It never dawned on me that model kit stuff might be broken on the new version. -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Feb 15, 2014, at 5:36

Re: [Jmol-users] Model Kit Bond Click

to Resolver. I've asked Markus about this, and he says it makes no sense to him, but there it is. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Feb 15, 2014, at 7:20 PM, Robert Hanson hans...@stolaf.edu wrote: just kidding. Much appreciated

Re: [Jmol-users] Spectra Predict Again

Bob, I think you're partly correct, but that error report is from your page. Actually, now that I think about it, you may be totally correct! Peter's test pages are 380X340. That may be more than just a suggestion. My page is tiny. Your page seems to be 300X300. Otis -- Otis Rothenberger o

[Jmol-users] Jspecview

Bob, Is the following correct in Jspecview hnmr? 1) Double click starts a measurement. 2) Subsequent double click continues a measurement. 3) Single click ends a measurement. Also, can you clear the screen of measurements? Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com

Re: [Jmol-users] Jspecview

is with JSmol, it's gone in iPad Air. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Feb 10, 2014, at 3:17 PM, Robert Hanson hans...@stolaf.edu wrote: Could be. Measurements are problematic. I'm not happy with the way it is, so feel free to give suggestions. Probably a set

Re: [Jmol-users] Jspecview

Oops, I left a word out - problem. Whatever the **problem** is with Safari/iPad2/JSmol, it's gone on iPad Air. On iPad 2 (after iOS 7), JSmol was almost useless - painfully slow and frequent Safari crashes. On iPad Air, it's just fine. Otis -- Otis Rothenberger o...@chemagic.com http

Re: [Jmol-users] Spectra Predict Again

656) Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Feb 9, 2014, at 10:09 PM, Robert Hanson hans...@stolaf.edu wrote: On Sat, Feb 8, 2014 at 7:36 PM, Otis Rothenberger osrot...@chemagic.com wrote: Bob, Error: Invalid negative value for rect attribute width=-51

Re: [Jmol-users] Spectra Predict Again

: Error: Invalid negative value for rect attribute width=-51 keep popping up as the page is used. This occurs on your test page also. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Feb 8, 2014, at 1:47 PM, Robert Hanson hans...@stolaf.edu wrote: What 2D conversion? I

Re: [Jmol-users] Spectra

script? Your js = Jmol._search; Jmol._search = function(applet, query) { unhideJSV(); js(applet, query); } seems to do it all - loading and syc. I'm missing something in this that does the sync. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Feb 6, 2014, at 9:49 AM

Re: [Jmol-users] Spectra

is not essential for me going to PubChem. For Resolver calls involving NIST, I need to do this. I'm not pulling IR and MS spectra from structured data files. I'm poking around NIST webpages, and the whole process is pretty nutty. Fortunately, NIST web pages are fairly structured. Otis -- Otis Rothenberger o

[Jmol-users] Spectra Predict Again

it that this means that the 2D to 3D (JME to Jmol) via Jmol.updateView(false) is not going via Resolver. Is that correct? Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- Managing the Performance of Cloud-Based

Re: [Jmol-users] Spectra

Bob, Yeah, from PubChem or ChemSpider. I don't get it. Is that all that's required - 2D into JSpecView? Or does JSME need the 2D even though I'm not displaying it? Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Feb 6, 2014, at 7:23 AM, Robert Hanson hans...@stolaf.edu

[Jmol-users] Spectra

is down. Models in the PubChem database are just fine for our small model homework exercises. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- Managing the Performance of Cloud-Based Applications

Re: [Jmol-users] Animating an IRC computed using Gaussian

of a proton, ;delay 3;echo;} if (i == 167){display *;echo regenerates the aromatic ring.;delay 3;} delay @{frameInterval}; } echo The final product is 1-chloro-4-methoxy-benzene.;delay 3;boundbox {*};centerat boundbox;zoom 0; Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Feb 2

Re: [Jmol-users] Animating an IRC computed using Gaussian

used as a template. He was doing some hide/show atoms in that previous animation. A funny thing happens when non-scripters play with this type of template: They love it! Tom went into an animation frenzy. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Feb 2, 2014, at 8:51

Re: [Jmol-users] Animating an IRC computed using Gaussian

evaluating frames for display once the file is loaded in Jmol??? But aside from that, isn't a frame a frame? Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Feb 2, 2014, at 10:15 AM, Rzepa, Henry S h.rz...@imperial.ac.uk wrote: On 2 Feb 2014, at 15:05, Otis Rothenberger osrot

Re: [Jmol-users] jmol-14.1.8_2014.02.01 -- Get your predicted NMR spectra here!

Robert and Robert, et al, Very, very, very, very nice! Thanks all Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Feb 1, 2014, at 2:54 PM, Robert Hanson hans...@stolaf.edu wrote: Robert Lancashire and I are happy to announce the first online open-source fully

Re: [Jmol-users] jmol-14.1.8_2014.02.01 -- Get your predicted NMR spectra here!

, but the basic idea works. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Feb 1, 2014, at 10:56 PM, Otis Rothenberger osrot...@chemagic.com wrote: Robert and Robert, et al, Very, very, very, very nice! Thanks all Otis -- Otis Rothenberger o...@chemagic.com http

Re: [Jmol-users] JSmol broken on Mac Safari back button

can also do this with JavaScript by defining an empty unbeforeunload function. I was never sure if either of these affected supporting files, however. I'm not sure you want to go this route. JSmol in user cache is a big plus. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com

Re: [Jmol-users] JSmol broken on Mac Safari back button

The only thing I can think is that it might be related to one of the page/Jmol loaded calls that I use: 1) body onload= 2) JSmol ready function 3) JSmol structure loaded callback Maybe also, server setting related to caching??? Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com

Re: [Jmol-users] Question: How is Info intended to be used?

the cookie jar. I did not realize what a pain a broken cookie jar could be for the user! Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Jan 28, 2014, at 12:16 PM, Angel Herráez angel.herr...@uah.es wrote: Hi, Chuck this is how I see it (but I may not be right

Re: [Jmol-users] Question: How is Info intended to be used?

Chuck, I'm sorry. I misunderstood. I thought you were trying to write Info variable data to Jmol.setInfo. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Jan 28, 2014, at 12:54 PM, Otis Rothenberger osrot...@chemagic.com wrote: Chuck and Angle, I think I'm in basic

Re: [Jmol-users] Jmol 14.0.6 released

is fairly simple molecules. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical

Re: [Jmol-users] Jmol 14.0.6 released

is the big issue for us: 1) With InChI, you can really do some nice searches. 2) With InChIkey, we can do grading of JSME structure and JSmol model questions on interactive pages. Not having to interrupt these if Resolver is down is a nice feature. Otis -- Otis Rothenberger o...@chemagic.com http

Re: [Jmol-users] Jmol 14.0.6 released

- just non-stereo SMILES. There may have been a recent change in this, but I don't think so. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Jan 21, 2014, at 3:13 PM, Philip Bays pb...@saintmarys.edu wrote: Bob: As I recall, several years ago you wrote the java applet

Re: [Jmol-users] Jmol 14.0.6 released

Afterthought: Phil, that's the neat thing about what Bob suggested. It takes unique SMILES off the table. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Jan 21, 2014, at 3:23 PM, Otis Rothenberger osrot...@chemagic.com wrote: Bob and Phil, Two responses here

Re: [Jmol-users] Jmol 14.0.6 released

the page until the script finishes. 3) pop-ups have to be set as ok for the page. 4) The SMILES really needs to be URL escaped. Pino, Put a model in a JSmol window and run that bottom script from the console to see what's going on. Otis -- Otis Rothenberger o...@chemagic.com http

Re: [Jmol-users] vibrate.htm for Gaussian output?

needed. I had some problems leaving it out, so I just continued to include it in my pages. If I have 10 JSmol objects in the body, I do 10 instantiations in the head. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Jan 16, 2014, at 9:00 AM, Kubasik, Matt mkuba

Re: [Jmol-users] Jmol.script() not returning

quote structure in the whole Jmol script. One thing that made issues go away for me completely is to simply use a function without an argument. That function, when called, can do anything you need done after the Jmol script executes. Otis -- Otis Rothenberger o...@chemagic.com http

Re: [Jmol-users] Jmol.script() not returning

made my problems go away - hence the function with no argument. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Jan 13, 2014, at 7:36 AM, Jaime Prilusky jaime.prilu...@weizmann.ac.il wrote: Have you tried it on 14.0.5 with HTML5? Jaim On Jan 13, 2014, at 2:26 PM

Re: [Jmol-users] Jmol.script() not returning

Jaim, Quick test on your side: Does alert(1234) work. No quotes - just alert(1234)? Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Jan 13, 2014, at 7:49 AM, Otis Rothenberger osrot...@chemagic.com wrote: I'm using 14.0.2. I can check out 14.0.5 later this morning. I

Re: [Jmol-users] jsmol problems

Rick, I can help you with #1. The following makes it go away: script type=text/javascript Jmol._alertNoBinary = false; jmolApplet0 = Jmol.getApplet(jmolApplet0, Info); /script Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Jan 10, 2014

Re: [Jmol-users] alertNoBinary

this approach before any global site changes. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Jan 10, 2014, at 3:55 PM, Spinney, Richard rspin...@chemistry.ohio-state.edu wrote: I can help you with #1. The following makes it go away: script type=text/javascript

[Jmol-users] Definitions

that I didn't know what I was talking about! I believe Bob has said that there really only is Jmol. I understand what he's saying with this, but that still leaves some term confusion. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com

[Jmol-users] Cross Domain Load

Bob, I could figure this out by trial and error, but you probably know the answer. Will JSmol load sdf text files cross domain? Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- Rapidly

Re: [Jmol-users] Cross Domain Load and Help Request

OK, Thanks. Are the following observations correct? Resolver does this. PubChem does this. RCSB does not do this. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Dec 30, 2013, at 12:45 PM, Robert Hanson hans...@stolaf.edu wrote: as long as the server is allowing full

Re: [Jmol-users] another Mac surprise

Safari and Firefox sharing the same Java cache??? This doesn't explain the object vs applet thing, however. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Dec 30, 2013, at 4:27 PM, Robert Hanson hans...@stolaf.edu wrote: It appears that Safari has a very strange feature

Re: [Jmol-users] another Mac surprise

Phil, Exactly. That's what I'm thinking. Safari won't cache it, but it will pull it from cache. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Dec 30, 2013, at 7:28 PM, J. Philip Bays pb...@saintmarys.edu wrote: I would think that they both rely on the java console. I

Re: [Jmol-users] JSmol popup menu on an iPad

The menu command will bring up the menu, but be careful. The command must be just menu - no trailing space or CR/LF caused by using [enter] in the console. The latter will throw an error. The bad news on an iPad is that the resulting menu does not respond to touches. Otis -- Otis Rothenberger

[Jmol-users] State and Triple Bond

) stateData = stateData.replace(/#/g, !HASH!); Since the state variable is used directly in Jmol to RESTORE model state, I now see why this had to be handled this way. Bottom Line: If you're looking for a triple bond # in a state file variable, look for %23, not #. Otis -- Otis Rothenberger o

Re: [Jmol-users] State Problem

to a new load seems strange, however. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Dec 9, 2013, at 9:25 PM, Otis Rothenberger osrot...@chemagic.com wrote: Bob, With our multi-user feature, I'm attempting to go back to state as the approach to save/load. I've got

[Jmol-users] State Problem

file: set defaultLattice {NaN NaN NaN}; It is the act of simply loading a model that breaks this line. There in no pattern - completely random. This is Mac Chrome with 14.0.1_2013.12.04. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com

[Jmol-users] State Question

and asp.NET scripting, so maybe it's unique to this configuration. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single

Re: [Jmol-users] final(?) testing: jmol-13.3.9_2013.12.03b

Bob and Phil, It looks like Resolver is down. Otis On Wed, Dec 4, 2013 at 7:34 AM, Philip Bays pb...@saintmarys.edu wrote: On Dec 4, 2013, at 12:50 AM, Robert Hanson hans...@stolaf.edu wrote: http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.12.03b.zip -- local installations Get

Re: [Jmol-users] final(?) testing: jmol-13.3.9_2013.12.03b

Yikes! Otis On Wed, Dec 4, 2013 at 10:34 AM, Robert Hanson hans...@stolaf.edu wrote: I have sent a note to Markus's former supervisor. (Markus has left NIH). On Wed, Dec 4, 2013 at 7:41 AM, Otis Rothenberger osrot...@chemagic.comwrote: Bob and Phil, It looks like Resolver is down

Re: [Jmol-users] progress ... ?

for downloading Safari 7. Perhaps we ought to bail on it for the moment to see what they are doing in Cupertino. I may drop by the Apple store today and ask some questions. Phil -- Otis Rothenberger o...@chemagic.com www.chemagic.com

Re: [Jmol-users] Safari test -- fixes Boolean issue?

/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger o...@chemagic.com www.chemagic.com

Re: [Jmol-users] Safari test -- fixes Boolean issue?

/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger o...@chemagic.com www.chemagic.com -- Otis Rothenberger o

[Jmol-users] 13.3.9_dev_2013.12.01 pdb alert pop up.

-- Otis Rothenberger o...@chemagic.com www.chemagic.com -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects

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