Re: [Jmol-users] Console Again

I can edit it, I should be able to place it and show/hide as I need. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jul 28, 2017, at 12:56 PM, Rolf Huehne <rolf.hue...@leibniz-fli.de> wrote: > > Am 28.07.17 um 18:35 schrieb Otis Rothenberger: >> A

Re: [Jmol-users] Console Again

, it’s not draggable on an iPad anyway. I am super impressed with how well Jmol works on an iPad. I’d like to add console control. I’m close! Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jul 28, 2017, at 3:18 PM, Rolf Huehne <rolf.hue...@leibniz-fli.de> wrote

Re: [Jmol-users] Console Again

More Info. I should have also checked this: jmolApplet0_console.innerText closehelp Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jul 28, 2017, at 2:14 PM, Otis Rothenberger <osrot...@chemagic.org> wrote: > > Rolf and Angel, > > OK, I’m close.

Re: [Jmol-users] Console Again

",20); $("#jmolApplet0_console").parent().css("position","fixed”) Inadvertently, and obediently, proves molApplet0_console is in my page. All my page content jumps to 20, 20, fixed. 3) jmolApplet0_console.innerText Unexpectedly, shows me that jmolApplet0_console.innerText is

[Jmol-users] Console Again

on","fixed", "important"); This is true with or without my adding to my page. Also, $("#JmolApplet0_console").length equals zero, which suggests that the div of that name does not exist. Again, this is all with the console

[Jmol-users] Console Question

with spartan should learn what spartan is producing. I know from correspondence with young model kit users that there is a sense that partial charge is some kind of atomic constant! Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org

[Jmol-users] iSpartan files and a question

le the student at Bradley got me started on this, it seems to me that iSpartan is a very nice low budget way to access spartan files that might be of interest to my secondary school low budget users. Otis -- Otis Rothenberger o...@chemagic.org

Re: [Jmol-users] Spartan Files

are working on. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jul 25, 2017, at 5:47 PM, Jennifer L. Muzyka <jennifer.muz...@centre.edu> > wrote: > > iSpartan doesn't do any calculations. It looks up data somewhere and only > works for the 50k in

[Jmol-users] Spartan Files

Jmol loads this file, but it is not currently loading charge info. While it does not look like there is enough mo info to plot homo/lumo, it does look like the charges should be Jmol readable. What do you think? Attachment coming via direct mail. Otis -- Otis Rothenberg

[Jmol-users] NIST Webbook

Bob may already know this. NIST WebBook has a spiffy new web page format. Some compound pages in the WebBook now have 2d and 3d SDF files with IR and other data in the files. The NIST on site 3d viewer is Jmol. Otis -- Otis Rothenberger o...@chemagic.org

[Jmol-users] PubChem Load

efore. In a conversation with PubChem, a staff member pointed me toward extracting data from the PubChem JSON files via a laborious loop. He pointed out that the structure of these files vary considerably from compound to compound. Indeed! Otis -- Otis Rothenberger o...@chemagic.org http://chemagi

Re: [Jmol-users] getting the applet ID

, open it up again, and continue a conversation. It also sends callback messages between windows, tabs, and frames. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jun 29, 2017, at 11:31 AM, Angel Herráez <angel.herr...@uah.es> wrote: > > Thanks, Bob > >

[Jmol-users] Invert Stereochemistry

Bob, I forget the limitations on invert stereochemistry. Should Jmol be able to handle 2-cyclohexylcyclohexanone? This is a situation where one of the moved atoms is part of ring that is not fused to chiral atom’s ring? Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org

Re: [Jmol-users] Find/chemical

megabyte in size. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jun 28, 2017, at 12:12 AM, Robert Hanson <hans...@stolaf.edu> wrote: > > I don't believe you can set the timeout for an AJAX call in a browser. Can > you? If so, we're not doing that but proba

[Jmol-users] Find/chemical

Bob, I assume calls like this {*}.find("chemical","stdinchi”) are using Ajax to Resolver. I see that I can catch a 404 error form this .find, but I’m wondering about a timeout. Do you have a timeout set in your Ajax call? If so, what’s the text response? Otis -- Otis

Re: [Jmol-users] Jmol SMILES Question

Excellent! I should have checked the docs. I have been using an incredibly clumsy way of doing this with Jmol/JSME, and it breaks on substituted allenes in JSME. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jun 9, 2017, at 12:09 AM, Robert Hanson <hans...@stol

[Jmol-users] Jmol SMILES Question

Bob, Can Jmol generate a non-stereo SMILES for a chiral model in the window? Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org -- Check out the vibrant tech community on one of the world's most engaging

[Jmol-users] Old Question

ring. Does this fall into the category of NOT best practice with @? Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.

[Jmol-users] Email List Error on My End

My email on the Jmol list was deactivated because emails sent to me were bouncing. The only way to test that I have this fixed is to post. So this is just a test... -- Otis Rothenberger o...@chemagic.org http://chemagic.org

Re: [Jmol-users] Jmol 14.13.1

e on {1 1 1}, but I suspect that Bob can answer this question. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Apr 10, 2017, at 2:02 PM, Pshemak Maslak <p...@chem.psu.edu> wrote: > > Otis and Dean, > > I just tested NaCl in JSmol (JavaSript) on a

Re: [Jmol-users] Jmol 14.13.1

the JSmol version. Is that correct? Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Apr 10, 2017, at 1:21 PM, Pshemak Maslak <p...@chem.psu.edu> wrote: > > Otis and Dean,, > > Thanks for the explanation. I was indeed able to find the whole command >

Re: [Jmol-users] Jmol 14.13.1

ore orientation; unitcell on; display cell=555; center visible; zoom 200; Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Apr 10, 2017, at 11:44 AM, Pshemak Maslak <p...@chem.psu.edu> wrote: > > Thank you Dean, > > I do not understand the > &

[Jmol-users] Question about JavaScript reader.readAsText(buFile, "UTF-8")

nyone know if this is the cross browser standard for this type of operation? Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org -- Check out the vibrant tech community on one of the world's most engaging tech sites, Sl

Re: [Jmol-users] Compare SMILES Question

Bob, Thanks. I have a student worksheet with Jmol and JME working together. I thought I had to change my JME aromatic setting, but it looks like I dob't have to do that. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Mar 30, 2017, at 12:33 AM, Robert Hanson &l

[Jmol-users] Compare SMILES Question

This is matching. Is that correct? Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link

Re: [Jmol-users] error in loading package.js

tionship? >From my very limited knowledge of permalinks, I think changing them is a big >no-no, but again I don't know much about them. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Dec 12, 2016, at 2:53 PM, pinostricc...@alice.it wrote: > > Dear frie

Re: [Jmol-users] Hack-a-mol

=68> There are many more formats than the basic documentation indicates. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Dec 8, 2016, at 9:19 AM, Robert Hanson <hans...@stolaf.edu> wrote: > > I'll leave that adaptation to you, Henry. :) > > On Thu, Dec 8, 2016

Re: [Jmol-users] Issue with

t/org/npentano.mol; wireframe 40;dots on;animation mode LOOP; animation on'", "Normal pentano") While it may not be obvious above, the "animation on" is followed by a single and double quote - i.e. on' " Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On

Re: [Jmol-users] JSmol submenus not working in iOS

n ISU Chemistry Department anniversary celebration. Were you even partly serious in your note? If so, I’ll pack it up when I get home. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Oct 20, 2016, at 11:12 AM, Greeves, Nick <ngree...@liverpool.ac.uk> wrote: > >

Re: [Jmol-users] JSmol submenus not working in iOS

mobile touch events, but I have not had time to play around with them on iPad. I don’t even know if they work on iPad. I mention this because touch and touch-hold are distinct events. Neither works with the Jmol menu. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Oct

Re: [Jmol-users] Java Applet Mouse problems in Firefox on MacOS 10.11.6

I cannot test item (b) fairly because I only have an Apple Magic Mouse, but (a) and (c) are both JSmol OK in El Capitan with Safari, FF, and Chrome. The browser versions are latest because they were just downloaded in the past few days. By OK, I mean translate - not zoom. Otis -- Otis

Re: [Jmol-users] Load JSmol from external host

Bob, Maybe your two answer emails reflect this, but did you catch my note about the current state of the sjmol.php call? This is currently http from Wikipedia. Is that what you want? Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Sep 10, 2016, at 9:08 AM, O

Re: [Jmol-users] Load JSmol from external host

0 0 0 0 0 0| -0.03921.1972 -0.8900 H 0 0 0 0 0 0 0 0 0 0 0 0| -1.98570.1365 -0. H 0 0 0 0 0 0 0 0 0 0 0 0| 1 2 1 0 0 0 0| 2 3 1 0 0 0 0| 1 4 1 0 0 0 0| 1 5 1 0 0 0 0| 1 6 1 0 0 0 0| 2 7 1 0 0 0 0| 2

Re: [Jmol-users] (no subject)

Interesting. That’s the JME Editor in the app. I don’t have an Android device, but from the developer photos, it’s JME. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Aug 25, 2016, at 8:14 AM, pinostricc...@alice.it wrote: > > Dear Friends, has any of you had t

Re: [Jmol-users] can't resize molecule in Jsmol window

? The framesets add a level of complexity that makes page layout more difficult and cross browser fussy. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Aug 17, 2016, at 9:32 AM, Jakubowski, Henry <hjakubow...@csbsju.edu> wrote: > > Hi all, > > Here is

[Jmol-users] Quiz Answers: Shhh, tell no one

tudents will be in Comedic Dire Straits (ouch)! Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level.

Re: [Jmol-users] JSME and SMILES

is don’t let a subset of students who may cheat taint the whole system. Just design things so that cheating carries a built in penalty and thus becomes irrelevant. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jul 20, 2016, at 8:39 AM, Jennifer L. Muzyka <jennif

Re: [Jmol-users] JSME and SMILES

Resolver (maybe PubChem) by an automated process would be a great real world project for one of the student teams. ( cc to Bob B) Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jul 19, 2016, at 8:22 PM, Jennifer L. Muzyka <jennifer.muz...@centre.edu> > wrot

Re: [Jmol-users] JSME and SMILES

Jennifer, On your page, students make several choices to set up a problem. It appears that each choice does a GET and reloads the page from sever with appropriate page modification. How hard would it be to return the correct SMILES on each of these GETS? Otis -- Otis Rothenberger o

Re: [Jmol-users] JSME and SMILES

. One more question, and then I'll do some more thinking. What other items or keys are in the database? Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jul 19, 2016, at 4:01 PM, Jennifer L. Muzyka <jennifer.muz...@centre.edu> > wrote: > > Otis, > 1200

Re: [Jmol-users] JSME and SMILES

JSME SMILES? Is there a possibility that the database creators may have drawn explicit hydrogens on carbon in non-stereo contect? Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jul 19, 2016, at 3:37 PM, Jennifer L. Muzyka <jennifer.muz...@centre.edu> > wrot

Re: [Jmol-users] JSME and SMILES

atter. Bob took the expression “unique SMILES” and made it obsolete! To do this (include stereochemistry via Bob’s approach) you will also have to make some options selections in JSME, but you will also be able to use E/Z and stereochemistry. How large is your SMILES database? -- Otis Roth

Re: [Jmol-users] Rapamycin

front door. I suspect, that this step is failing with the return of the 2D. Recall that CORINA needs to break molecules into known ensembles which are then reassembled as 3D. FYI, CORINA DOCS. I have no clue what’s going on in SPARTAN. Otis -- Otis Rothenberger o...@chemagic.org http

Re: [Jmol-users] JSME and SMILES

nd approach comes into play - my previous email. I’ve been using a Jmol/JSME SMILES comparison for quite a while, so don’t hesitate to ask if you need more specific information. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jul 18, 2016, at 4:22 PM, Otis Rothe

Re: [Jmol-users] JSME and SMILES

MILES \ notation into a JavaScript string - i.e. correct the fact that \ in a character escape in JavaScript. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jul 18, 2016, at 3:39 PM, Jennifer L. Muzyka <jennifer.muz...@centre.edu> > wrote: > > I’m not sure i

Re: [Jmol-users] Capture PNGJ file as a variable

key, but the _IMAGE_ key does not seem to be there. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jul 15, 2016, at 4:51 AM, Angel Herráez <angel.herr...@uah.es> wrote: > > El 14 Jul 2016 a las 12:13, Robert Hanson escribió: >> Note that b

Re: [Jmol-users] MF function question...

Bob, Thanks, that email is a big help on the @ usage. Otis --Otis rothenbergero...@chemagic.org http://chemagic.org > On Jul 8, 2016, at 9:19 AM, Robert Hanson wrote: > > > Happy to address that. @ is tricky because it has multiple uses: > > > 1. Original use:

[Jmol-users] MF function question...

ray confusion into the JavaScript side. It’s not a big deal, but I just got hung up on .size vs .length. In the case at hand, I’m replacing a Jmol.getPropertyAsJavaObject approach to mf with Jmol.evaluateVar approach to mf. Otis -- Otis Rothenberger o...@chemagic.org http:/

Re: [Jmol-users] [n = {*}[0].molecule;show n] bug

Excellent. That works. Related to the mf array this leads to, what’s the best way to hand a JmolScript array to a page JavaScript function? The only way I know how to do this is with Message Callback. Is there a more direct way? Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org

Re: [Jmol-users] [n = {*}[0].molecule;show n] bug

Maybe this is a Safari thing. I worked on this some more today, and I’m seeing erratic n=1 in other cases not involving obvious presence of partial charge. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jun 29, 2016, at 10:53 PM, Robert Hanson <hans...@stolaf.edu&

Re: [Jmol-users] [n = {*}[0].molecule;show n] bug

carries with it the {*}[0].molecule problem. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jun 29, 2016, at 8:52 AM, Robert Hanson <hans...@stolaf.edu> wrote: > > I'll check on what's up with the partial charges. No effect on > {molecule=1}.find("M

[Jmol-users] [n = {*}[0].molecule;show n] bug

lly, it seems to me that if CH2 is in the Jmol window, then a simple extraction of mf should be CH2 - not CH4. I’m just saying. This, of course, is a small molecule guy’s opinion! Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.

Re: [Jmol-users] page-developer request - Jmol Unplugged

is also a component of my BCCE presentation. My plan all along was to give this thing to folks who want it, so that fits in well with your suggested approach. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jun 28, 2016, at 9:00 AM, Robert Hanson <hans...@stol

Re: [Jmol-users] RCSB

Phil, In my attempt to locate my [n={*}[0].molecule;show n] problem mentioned in a previous email, I downloaded today’s version. I can confirm pdb load problem. The console says the pdb is loaded, but nothing is visible. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org

Re: [Jmol-users] Molecular Formula Problem Related to Breaking a Bond

Bob, > > {*}[0] > Agree: It appears to generate the atomIndex of the last atom. > {*}[0].molecule > I don’t think so: It consistently generates the number 1 for any number of fragments in the window. On the other hand, using the infinite number of monkeys writing Shakespeare approach,

Re: [Jmol-users] Molecular Formula Problem Related to Breaking a Bond

molApplet0, "moleculeInfo.mf").toString() gives “saturated” mf values. I need to sleep on it. Maybe I can pick the correct formulas out with the value of n from Jmol.getPropertyAsJavaObject(jmolApplet0, "moleculeInfo.mf").modCount.toString() using x = {molecule=#}.find("

[Jmol-users] Molecular Formula Problem Related to Breaking a Bond

. This all relates to mass spec study in the model kit. The bond is being broken by set picking assignBond_0. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org -- Attend Shape: An AT Tech Expo July 15-16. M

Re: [Jmol-users] Jmol 14.6.0_2016.06..22

Bob, Click-invert, compare: Identical, Enantiomers, and Diastereomers are all now working. Thanks… Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jun 23, 2016, at 9:37 AM, Robert Hanson <hans...@stolaf.edu> wrote: > > Jmol.___JmolVersion="14.6.0_2016

Re: [Jmol-users] Compare Seems to Be Broken 14.6.0_2016 05 24

Bob, If it helps, 14.4.4_2016.03.25 is a few days after you fixed the click invert and compare IS WORKING in this version. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jun 16, 2016, at 3:40 PM, Otis Rothenberger <osrot...@icloud.com> wrote: > > Bo

[Jmol-users] Compare Seems to Be Broken 14.6.0_2016 05 24

following line in SmilesMatcher.js was affected by the click inversion fix? check = (this.areEqual ("/invertstereo/" + smiles2, smiles1) > 0); Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org

Re: [Jmol-users] Load URL

Rothenberger o...@chemagic.org http://chemagic.org > On Jun 13, 2016, at 8:42 PM, Robert Hanson <hans...@stolaf.edu> wrote: > > > > On Mon, Jun 6, 2016 at 10:25 PM, Otis Rothenberger <osrot...@icloud.com > <mailto:osrot...@icloud.com>> wrote: >

Re: [Jmol-users] updating SpectralZoo problems

structure button is loading a new page! Are you using GoDaddy by any chance? Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jun 13, 2016, at 10:18 AM, Otis Rothenberger <osrot...@icloud.com> wrote: > > Hi Jennifer, > > I hate to be a "poop,&quo

Re: [Jmol-users] updating SpectralZoo problems

Hi Jennifer, I hate to be a "poop," but even with cache clearing this page is still not working for me on Safari or Windows 10 Edge: http://chemserv.centre.edu/muzyka/spectralzoo/jsmol/specZoo.php Is this the page that you were referencing in your latest note? Otis -- Otis Roth

Re: [Jmol-users] updating SpectralZoo problems

Jennifer, In the jsmol folder, Bob has this file: jsv_mol.htm It’s probably the original of the file link in my previous email. This one is slightly more commented, and one comment explains the short list of js files vs the long list of js files. Otis -- Otis Rothenberger o

Re: [Jmol-users] updating SpectralZoo problems

ot;, MInfo)); $("#jsvdiv").html(Jmol.getJSVAppletHtml("jsvApplet0",SInfo)); }); This suggests timing is important. I hope this helps! It has certainly been instructive on my end. -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jun 10, 2016, at 2:19 PM

Re: [Jmol-users] updating SpectralZoo problems

(jmolApplet2,'load files/structure/triClEthane.PDB’); I wonder if you need one of the Jmol ready functions to load this if JSV is in the picture?? StOlaf server is down right now. I’ll look into this later and get back to you. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jun

Re: [Jmol-users] updating SpectralZoo pages

Hi Again Jennifer, I spent some time looking at your code. You have a lot going on with JQuery, JQuery UI widgets, and Bootstrap. I think I see other possible conflicts in addition to the possible unquote attribute issue. You are loading your own version of JQuery (along with the UI Widgets).

Re: [Jmol-users] updating SpectralZoo pages

with this unquoted id? I’ll keep looking at your page code, but it looks to me like JSmol is loading, but id=jsvdiv is not getting its HTML. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jun 9, 2016, at 3:30 PM, Jennifer L. Muzyka <jennifer.muz...@centre.edu> > wr

Re: [Jmol-users] individual atom color

Oops... This is the more complete version of that color link: http://jmol.sourceforge.net/jscolors/ Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jun 7, 2016, at 8:58 AM, Otis Rothenberger <osrot...@icloud.com> wrote: > > Km, > > Providing that

Re: [Jmol-users] individual atom color

of this second line. Here is a useful Jmol color chart: http://www.biorom.uma.es/contenido/biomodel/Jmol/colors/jmol_colors.en.htm Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jun 7, 2016, at 5:39 AM, Krishna Mohan <krishna.mo...@mbcet.ac.in> wrote: >

[Jmol-users] Load URL

will a local file entry into Jmol.loadFileFromDialog(jmolApplet0) dialog look for jsmol.php. I assume a binary file needs to go to jsmol.php. Is that correct? Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org

Re: [Jmol-users] dipole examples page

enabled in the browser preferences. I’ve completely abandoned Java Jmol in favor of JSmol (javascript Jmol), so I can’t be of much help with Java version problems. Sorry... Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jun 2, 2016, at 2:58 PM, John Keller <

Re: [Jmol-users] Jmol for mac installation

be happy to make a zip file available for testing. My target date is a presentation at the August BCCE meeting, but I have a testable version now. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jun 1, 2016, at 3:41 PM, John Keller <jwkel...@alaska.edu> wrote: &g

Re: [Jmol-users] [Jmol-developers] myJmol as variable in Jmol.script

Angel and Klaus, These two commands should pretty much take mouse zoom out of the picture: unbind _wheelZoom unbind _slideZoom The single command unbind should turn zoom back on. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On May 21, 2016, at 5:57 AM, Angel Herr

[Jmol-users] Interesting PubChem Error Note

1 Code: PUGREST.Unimplemented Message: Cannot (yet) generate 3D coordinates for structures without an existing CID Stay Tuned… Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org -- Mobile security can be enabling, not

Re: [Jmol-users] Interesting PubChem Discovery

You’re going to have to copy/paste that last link! -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On May 17, 2016, at 2:12 AM, Otis Rothenberger <osrot...@icloud.com> wrote: > > http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/PNG?smiles=C/C(C)=C/C(C%5BC@@H

[Jmol-users] Interesting PubChem Discovery

thin PubChem. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org -- Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the impos

Re: [Jmol-users] SMILES and SMARTS problems

nih.gov/chemical/structure/C1=CC=CC(O)=C1/aromatic <https://cactus.nci.nih.gov/chemical/structure/C1=CC=CC(O)=C1/aromatic> YES Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On May 16, 2016, at 1:49 PM, Otis Rothenberger <osrot...@icloud.com> wrote: > >

Re: [Jmol-users] SMILES and SMARTS problems

tic". END QUOTE In a 2007 blog, Rich Apodaca (ChemWriter Application) took a look at the history of SMILES and aromaticity. It’s an interesting read: http://depth-first.com/articles/2007/11/28/smiles-and-aromaticity-broken/ <http://depth-first.com/articles/2007/11/28/smiles-and-aromaticity-b

Re: [Jmol-users] fun with Jmol -- xxxx.find("chemical",...)

Thanks Daniel, that’s good to know. Pierluigi, take note of this re your suggested use of standard InChI. It looks like that’s a go for string comparison. On canonical SMILES, Bob made them irrelevant inside Jmol. I still don’t understand how it works, but it works! Otis -- Otis Rothenberger

Re: [Jmol-users] fun with Jmol -- xxxx.find("chemical",...)

e can be converted into a full structure representation if they are present in the database. So Daniel and I thought, combining both things would generate a very powerful tool for name-to-structure conversion.” Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On May 10, 2016, at

Re: [Jmol-users] fun with Jmol -- xxxx.find("chemical",...)

? By identity, I mean the same kind of connective identity that could be established with a stereo SMILES comparison. If there is uncertainty in the above InChI comparison, would pulling the **standard** InChI from a single source like Resolver improve the comparison? Otis -- Otis Rothenberger o

Re: [Jmol-users] fun with Jmol -- xxxx.find("chemical",...)

=name_by_opsin https://cactus.nci.nih.gov/chemical/structure/1-butanol/stdInChI?resolver=name_by_database Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On May 10, 2016, at 6:08 AM, Pierluigi Quagliotto > <pierluigi.quaglio...@unito.it> wrote: > > 1) 7-et

Re: [Jmol-users] Let's Not Forget PubChem

the name app that uses this approach. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On May 10, 2016, at 12:31 AM, Otis Rothenberger <osrot...@icloud.com> wrote: > > OK, I promise I’ll drop this subject

Re: [Jmol-users] Let's Not Forget PubChem

are on the page under the JSME app. For a real head to head competition treat, simply draw one cyclobutane ring, or one cyclooctane ring, or one cyclopenta-1,3-diene ring, or oct-1-yne, or spiro[2.2]pentane... I’m just "sayin" Otis -- Otis Rothenberger o...@chemagic.org http://ch

Re: [Jmol-users] Let's Not Forget PubChem

} I definitely got the impression that the compound to compound variation was by design. If not by design, then it must be related to the evolution of their system. Either way, they definitely know about it. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On May 9

[Jmol-users] Let's Not Forget PubChem

ion from the JSONP above is tricky because these PubChem data files are not consistent from compound to compound. You must, therefore, iterate through the data in a loop to cherry pick what you want. If anyone wants this extraction code, I’d be happy to post it. It’s not lengthy code. Otis -- O

Re: [Jmol-users] fun with Jmol -- xxxx.find("chemical",...)

. If you find any mistakes, please tell us. Our plan is to improve the name index over the time but we are of course happy about any contributions helpful for this process. Thanks!” And yes, he is talking about trivial AND IUPAC names above. Otis -- Otis Rothenberger o...@chemagic.org http

Re: [Jmol-users] fun with Jmol -- xxxx.find("chemical",...)

if you want to go either route. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On May 8, 2016, at 3:23 PM, Pierluigi Quagliotto > <pierluigi.quaglio...@unito.it> wrote: > > Dear Bob, > > Last year I developed my teaching site: > > http

Re: [Jmol-users] SMILES and SMARTS problems

, ''); ans = ans.replace(/\\/g, ''); return jmv("'" + key + "'.find('SMILES','" + ans + "') > 0"); } If you need further explanation, let me know. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On May 6, 2016, at 11:00 AM, Mike Cas

Re: [Jmol-users] jmolApplet0 spin rate/frame rate

ond] Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On May 1, 2016, at 9:04 PM, mark <m...@haunted-river.net> wrote: > > Hello, > > Traditionally I have used jsmol.lite and I was able to set these > parameters from the info block. I decided that I w

Re: [Jmol-users] MEP

Angel, Please check me on the syntax of what I'm suggesting below. I usually do this with molfiles - not mol2 Birgit, I'm not sure why you want to store the Jmol mep data in the mol2 file, but here is an approach that will work. You can store jmol script in a mol2 file that will automatically

Re: [Jmol-users] MEP

. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On May 1, 2016, at 3:08 PM, Birgit Lachner <bir...@lachner-net.de> wrote: > > Dear Robert and Angel, > > your informations are really very interessting. The two commands to calculate > and show the ME

Re: [Jmol-users] Flat structures

e data in the 3d “SDF” above: (-)-carvone by the way! Here’s the 2D “SDF" https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/439570/record/JSON/?record_type=2d_type=display <https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/439570/record/JSON/?record_type=2d_type=display> Otis --

[Jmol-users] load JME file issue

1 23 25 2 24 26 2 46 60 1 7 47 1 8 66 1 9 64 1 15 16 2 20 21 2 25 26 1 1 67 -1 3 68 1 5 69 -1 7 70 1 48 33 1 8 71 1 49 34 1 9 72 1 10 73 1 11 74 1 50 35 1 61 36 1 -- Otis Rothenberger o...@chemagic.org http://chemagic.org

Re: [Jmol-users] JSME Fun

hlight, AtomClicked, BondClicked I was aware of these other JSME callbacks, but I tend to have tunnel vision when a potential simple “model kit” use is a possibility! Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Apr 28, 2016, at 11:38 PM, Robert Hanson <hans...@stolaf.edu&

[Jmol-users] JSME Fun

Just start drawing in the JSME window. Great fun… There are some loaded Jmol model issues via this route. I’ll try to figure them out and then ask Bob! Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org -

Re: [Jmol-users] New iPad

pretty straight forward. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Apr 22, 2016, at 6:33 PM, J. Bays <pb...@saintmarys.edu> wrote: > > When you buy one of these, what storage do you get:32, 64, 128..? > > J. Philip Bays > Emeritus Profes

[Jmol-users] New iPad

(read and write) when you’re on line, so if your page uses full url’s for server calls, you're in business. If you try any of this on a Mac or an iPad, Apple is case sensitive when if comes to the file names on the localhost. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org

Re: [Jmol-users] Background Color

> On 04/22/2016 10:39 PM, Otis Rothenberger wrote: >> Does anyone know how to GET the existing background color in Jmol Script? I >> looked through the getProperty docs, and I can’t see any access to the >> existing background color. I can set a global in the load script to sol

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