Re: [Jmol-users] Some Desirable Features!

eded, and the functions inside the Jmol object take care of business from there. This is consistent with other paradigms for programming in Javascript, such as those associated with jQuery UI and Bootstrap JS. The first paragraph of this page provides some rationale too. Cheers, Mike Michael E

Re: [Jmol-users] Jmol/JSmol 3.2.4 and 3.3.4 released

ww.metallacycle.com/lib/jquery.min.map 404 (Not Found)"--maybe a .map where a .js should be? Cheers, Mike Michael Evans Freshman Chemistry Lab Coordinator Georgia Institute of Technology (502) 439-2540 | mevan...@gmail.com On Aug 23, 2013, at 1:44 PM, Robert Hanson wrote: > Jm

Re: [Jmol-users] FirstGlance in Jmol: Enhanced (Again)

Eric, You should give JSmol a try! Depending somewhat on the complexity of your code, I think you'll find the switch pretty easy... :-) For me a few mass find/replaces did the trick. Cheers, Mike --- Michael Evans Department of Chemistry University of Illinois, Urbana-Champaign On Sun, J

Re: [Jmol-users] JSmol on iPAd

Just tested on an iPad 2, and the demos (test2.htm and simple2.htm) are working for me. Cheers, Mike --- Michael Evans Department of Chemistry University of Illinois, Urbana-Champaign On Wed, May 1, 2013 at 5:12 PM, Robert Hanson wrote: > thanks for the tip -- what page was that? > &g

Re: [Jmol-users] Freeze a Model?

Thanks for the tips, Otis & Angel! I'll try these out when I get a chance. Cheers, Mike --- Michael Evans Department of Chemistry University of Illinois, Urbana-Champaign On Sat, Apr 27, 2013 at 7:34 AM, Otis Rothenberger wrote: > Michael, > > I'm not sure if you mean

[Jmol-users] Freeze a Model?

how to handle the underlying logic of testing whether the atomic positions of the two models match, but I don't know if one of two models in the Jmol window can be frozen in place. Any idea if this is possible, and if so, how it could be done? I'd rather not resort to two separate applets.

Re: [Jmol-users] Searching for help

Whomp, I stand corrected! Thanks, Angel and Otis. Cheers, Mike --- Michael Evans Department of Chemistry University of Illinois, Urbana-Champaign On Thu, Apr 25, 2013 at 2:45 PM, Otis Rothenberger wrote: > Hi Birgit, > > Jmol can calculate MMFF94 partial charges. The following scri

Re: [Jmol-users] Searching for help

cular orbitals and electrostatic potential. The output can be downloaded. I could be wrong, but I *think* the .MO files that come out of a Mopac WebMO job contain information about electrostatic potential. Cheers, Mike --- Michael Evans Department of Chemistry University of Illinois, Urbana-Cham

Re: [Jmol-users] scriptWait and scriptWaitAsArray

Wow, where have I been? This works great. Works really well for grabbing orientation info too. Thanks, Bob. Cheers, Mike --- Michael Evans Department of Chemistry University of Illinois, Urbana-Champaign On Mon, Mar 25, 2013 at 5:23 PM, Robert Hanson wrote: > Well, you know, since JSmol

[Jmol-users] scriptWait and scriptWaitAsArray

thing like this, I'd love to know. Cheers, Mike --- Michael Evans Department of Chemistry University of Illinois, Urbana-Champaign -- Own the Future-Intel® Level Up Game Demo Contest 2013 Rise to greatness in Inte

Re: [Jmol-users] super light-weight JSmol?

; zoomScaling: 1.5, > pinchScaling: 2.0, > mouseDragFactor: 0.5, > touchDragFactor: 0.15, > multipleBondSpacing: 4, > > Be sure to try it on your smart phone. > > Comments? Suggestions? > >

Re: [Jmol-users] Jmol | lcaocartoon

lobes can be drawn and oriented (per demand) > using "isosurface" command, but the lonepair dots are much harder if one > wants them to keep up with molecular rotations and not eclipse each other > at some orientations. > > Is there a simple way to deal with these issues? &g

Re: [Jmol-users] Jmol | lcaocartoon -sp3d Issue

ttp://chemapps.stolaf.edu/jmol/jsmol.zip > > > Bob > > > On Sun, Mar 10, 2013 at 2:19 PM, Michael Evans wrote: > >> Jmol'ers, >> I am having trouble using lcaocartoon in a very specific case. If you >> look on this page, the antibonding orbitals render

[Jmol-users] Jmol | lcaocartoon -sp3d Issue

success: http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm An sp3d lobe renders fine, but nothing happens when I try lcaocartoon create "-sp3d". Am I missing something? Cheers, Mike --- Michael Evans Department of Chemistry University of I

Re: [Jmol-users] Nested quotes problem

ity of Liverpool > Donnan and Robert Robinson Laboratories > > Crown Street, LIVERPOOL L69 7ZD U.K. > Email address:ngree...@liverpool.ac.uk 'ngree...@liverpool.ac.uk');> > WWW Pages:http://www.chemtube3d.com > Tel:

Re: [Jmol-users] hmm. css question

> > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > -- --- Michael Evans Department of Chemistry University of Illinois, Urbana-Champaign -

Re: [Jmol-users] JSMol not working with JSmol.min.js

Works for me, big guy. The page loads using Java but the HTML5 Version link works fine for me. Cheers, Mike --- Michael Evans Department of Chemistry University of Illinois, Urbana-Champaign On Wed, Feb 27, 2013 at 3:16 PM, Daniel Barich wrote: > My page is still not working, and neither

Re: [Jmol-users] WebMO

BTW, I lived at Centre for the Governor's Scholars Program back in 2003. Hard to believe it's been ten years since then...I'm sure the campus is as beautiful as ever! Cheers, Mike --- Michael Evans Department of Chemistry University of Illinois, Urbana-Champaign On Fri, Feb 22, 2013 a

Re: [Jmol-users] JSmol "lite"

Agreed, Otis. I realized after reading your message that a version of JSmol that worked that way would be highly desirable, provided the process of loading files as needed is acceptable from a user experience perspective. Cheers, Mike --- Michael Evans Organic Chemistry Graduate Student, Moore

Re: [Jmol-users] JSmol "lite"

ctionality as > needed.) > > Bob > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Chemistry Department > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, &

Re: [Jmol-users] can you visualize more than one molecular orbital at a time?

Definitely possible! Use "isosurface surf1 mo 3" and "isosurface surf2 mo 5," for example. Cheers, Mike On Monday, January 28, 2013, Jonathan Gough wrote: > I know you can show a single MO (from a gamess log file), but is there a > way to visualize 2 of them simultaneously? > > For example if I

Re: [Jmol-users] JSmol | Quirky Behavior of "Zoom" Command

t; > > although the following does not properly wait: > > script: "set antialiasDisplay;background white;load caffeine.mol;zoomTo 2 > 50;background blue" > > > > On Sat, Jan 26, 2013 at 4:33 AM, Michael Evans wrote: > > I am...I should be a little more specific.

Re: [Jmol-users] JSmol | Quirky Behavior of "Zoom" Command

Hanson wrote: > I'm certainly not seeing that. Are you using the latest at > http://chemapps.stolaf.edu/jmol/jsmol.zip ? > > > On Fri, Jan 25, 2013 at 10:06 PM, Michael Evans > > > wrote: > >> Hey all! In JSmol, running the "zoom" command re

[Jmol-users] JSmol | Quirky Behavior of "Zoom" Command

s from Jmol to JSmol using find/replace and regular expressions, this bug/feature/potentiality had me beating my head against the wall. Cheers, Mike --- Michael Evans Organic Chemistry Graduate Student, Moore Group University of Illino

Re: [Jmol-users] JSmol update

Bob, Not sure if I'm the only one having this problem, but I can't get jsmol.zip to decompress properly. On OS X 10.8.2, Archive Utility hangs while trying to unzip it. I both hope and don't hope it's just me! :-P Cheers, Mike --- Michael Evans Organic Chemistry Graduate

Re: [Jmol-users] JSmol popup menu and console

Phil, Don't forget that you can left-click or tap on the JSmol logo to pull up the context menu. No right-click required! :-) Cheers, Mike --- Michael Evans Organic Chemistry Graduate Student, Moore Group University of Illinois, Urbana-Champaign On Wed, Jan 2, 2013 at 2:50 PM, Philip

Re: [Jmol-users] JSmol popup menu and console

ntextmenu", function(ev) { // right-click ev.preventDefault(); var xym = Jmol._jsGetXY(ev, canvas); canvas.applet._applet.viewer.handleOldJvm10Event(org.jmol.api.Event.MOUSE_UP,xym[0],xym[1],org.jmol.api.Event.MOUSE_RIGHT,System.currentTimeMillis()); }); Cheers, Mike --- Michael Evans Organic

Re: [Jmol-users] Jmol | Context Menu for JSmol

mol/jsmol/test2.htm?USE=HTML5 > > > On Sun, Dec 23, 2012 at 11:08 PM, Robert Hanson wrote: > > OK! We have a popup menu in JavaScript. Thank you, Michael Evans!!! jQuery > UI to the rescue. All relevant code is in jsmol/j2s/java/coremenu.js > > > Check it out. http://chema

Re: [Jmol-users] Jmol | Context Menu for JSmol

Yep, the link below is still the latest. If you can see the radio button group of colors, you know you're looking at the newest version. I've also just implemented ImageIcon. http://www.metallacycle.com/play/netmol/tests/popupMenu/popupMenu.html Cheers, Mike --- Michael Evans Organic

Re: [Jmol-users] Jmol | Context Menu for JSmol

ect. Cheers, Mike On Friday, December 21, 2012, Bob Hanson wrote: > What's the latest? I'd like to test this some tomorrow. > > Sent from my stupid iPhone > > On Dec 19, 2012, at 5:56 PM, Michael Evans wrote: > > Guess I was feeling lazy when I wrote menuRemoveIte

Re: [Jmol-users] Jmol | Context Menu for JSmol

code (probably don't have to tell you that... :D). Cheers, Mike --- Michael Evans Organic Chemistry Graduate Student, Moore Group University of Illinois, Urbana-Champaign On Wed, Dec 19, 2012 at 3:05 PM, Robert Hanson wrote: > Wow, this is great! Almost there, I think. > > > On

Re: [Jmol-users] Jmol | Context Menu for JSmol

Great question, Phil...perhaps a left-click on the JSmol frank a la Jmol would work? --- Michael Evans Organic Chemistry Graduate Student, Moore Group University of Illinois, Urbana-Champaign On Wed, Dec 19, 2012 at 3:34 PM, Philip Bays wrote: > How does this work on a tablet or my

Re: [Jmol-users] Jmol | Context Menu for JSmol

here are any JS event experts out there, help would be appreciated! :-) Is this what you had in mind, Bob? Cheers, Mike --- Michael Evans Organic Chemistry Graduate Student, Moore Group University of Illinois, Urbana-Champaign On Wed, Dec 19, 2012 at 9:10 AM, Michael Evans wrote: > Thanks,

Re: [Jmol-users] Jmol | Context Menu for JSmol

Thanks, Bob. I got the sense objects would be the way to go. Working on this this morning. Stay tuned! --- Michael Evans Organic Chemistry Graduate Student, Moore Group University of Illinois, Urbana-Champaign On Wed, Dec 19, 2012 at 8:56 AM, Robert Hanson wrote: > OK, Michael, here

[Jmol-users] Jmol | Context Menu for JSmol

hts on the best way to implement addItem. Cheers, Mike --- Michael Evans Organic Chemistry Graduate Student, Moore Group University of Illinois, Urbana-Champaign -- LogMeIn Rescue: Anywhere, Anytime Remote support for

Re: [Jmol-users] R: Re: R: Re: R: JSmol -- Are we done?

Exactly. Creating the nested unordered list is straightforward; perhaps only the Menu component of jQuery UI will be necessary. Stay tuned. --- Michael Evans Organic Chemistry Graduate Student, Moore Group University of Illinois, Urbana-Champaign On Mon, Dec 17, 2012 at 12:37 PM, Robert

Re: [Jmol-users] R: Re: R: Re: R: JSmol -- Are we done?

ils? Let me know when you get a chance. Thanks! Cheers, Mike --- Michael Evans Organic Chemistry Graduate Student, Moore Group University of Illinois, Urbana-Champaign On Sun, Dec 16, 2012 at 2:30 PM, Robert Hanson wrote: > continuing this thread -- The only things missing from JSmol

Re: [Jmol-users] JSmol core libraries

Wow, I do notice a significant drop in loading speed (OS X 10.8, Chrome). Thanks, Bob! Cheers, Mike --- Michael Evans Organic Chemistry Graduate Student, Moore Group University of Illinois, Urbana-Champaign On Sat, Dec 15, 2012 at 3:45 PM, Robert Hanson wrote: > > I have redeployed

Re: [Jmol-users] Signed Applet Using 13.0 JS

Gotcha. Thanks, Bob. Cheers, Mike On Sep 20, 2012, at 10:53 PM, Robert Hanson wrote: > Oh, THAT message > > Hmm. I certainly use Jar files not in the current directory. Oh, I know. > There are two Info parts now: > > Info.jarPath > Info.jarFile > > just make sure you put the full path i

Re: [Jmol-users] Snow Leopard/Lion vs. Jmol?

Eric et al, I would head for Mountain Lion. Java on Lion was a little spotty for me, especially while using Safari. I don't know if Lion supports Safari 6 now, but many of the slow downs and hangs I experienced in Lion with Safari 5 went away upon upgrading to Safari 6. Google Chrome was old reliab

Re: [Jmol-users] Jmol back button

Martin, You could use HTML5's local storage capabilities or server-side storage in a session variable to do this, but I don't think there's a simple way to do it using Jmol. You would use Jmol to set up a callback, however—probably a scriptCallback. In the callback function, you could save the stat

Re: [Jmol-users] How to align 2 PDBs with the Jmol

Kumardeep, I'm unsure of Jmol's ability to read PSE files, but if you are not married to the superposition software, Superpose from the University of Alberta is a nice alternative. The output of Superpose is a multi model PDB file, which you can play with using Jmol's model command. Cheers, Mike O

Re: [Jmol-users] renaming Object Jmol files

A good idea from the standpoint of loading speed. Cheers, Mike --- Mike Evans Organic Chemistry Graduate Student, Moore Group University of Illinois, Urbana-Champaign On Thu, Jun 14, 2012 at 4:30 PM, Paul Pillot < paul.pil...@ac-orleans-tours.fr> wrote: > Good idea ! > Shall we bundle them in

Re: [Jmol-users] Announcement of Jmol based Webinterface to simulate nanowire biosensors

Martin—link...? I'd love to try this out. Cheers, Mike --- Mike Evans Organic Chemistry Graduate Student, Moore Group University of Illinois, Urbana-Champaign On Fri, May 11, 2012 at 10:26 AM, Martin Hediger wrote: > Dear Jmol Users > In our research group we have developed a web application

Re: [Jmol-users] Jmol Load in Safari and Firefox

To piggyback on Martin's observation, Chrome does the same to me on OS X 10.7.3. It's been this way for a long time...since the beginning of 12.2, IIRC. But it's been brought up a couple of times before, and I think we concluded it's a browser issue? Cheers, Mike --- Mike Evans Organic Chemistry

Re: [Jmol-users] Loading a Remote File After an Update

t; you have to change the name in an innocuous way, with a ? : > > load myfliles.jmol?2234902394 > > the server needs to not care about the "?" query business and return the > .jmol file anyway. the browser will cache the files as different temporary > files. > > >

[Jmol-users] Loading a Remote File After an Update

Hey all, I'm having a little issue involving updates to script files on the web that a loaded Jmol applet does not appear to "see." The change is only "noticed" by Jmol after I restart my web browser, as if the file is cached somehow. There may be no way around this issue if it's the way the brows

Re: [Jmol-users] How to hide the Jmol logo

Offend?! I think the rest of the jmol-users listserv just finds the whole exchange hilarious. :-) Cheers, Mike --- Mike Evans Organic Chemistry Graduate Student, Moore Group University of Illinois, Urbana-Champaign On Fri, Feb 10, 2012 at 2:56 PM, Jeff Hansen wrote: > I just did too. Didn't

[Jmol-users] SSL Encryption and Jmol Applets

Hello all—I'm serving a ton of Jmol applets through a wiki that employs SSLv3 encryption. These applets suddenly broke, giving a "bad_record_mac" error, when we updated to SSLv3 on campus due to a bug (see below). As a result of this bug, CITES has modified all of our web server > configurations t

Re: [Jmol-users] getProperty Image

nd upcoming > releases of 12.3.12 and 12.2.12. > > Sent from my stupid iphone > > On Jan 12, 2012, at 11:40 PM, Michael Evans wrote: > > Lords & lasses of Jmol—just wanted to note an issue in 12.2.11 that I > think Dr. Gutow mentioned for 12.2.10 back in December..."getPro

[Jmol-users] getProperty Image

Lords & lasses of Jmol—just wanted to note an issue in 12.2.11 that I think Dr. Gutow mentioned for 12.2.10 back in December..."getProperty image" and the Javascript equivalent jmolGetPropertyAsString('image', 'all') cause the applet to hang. Is there a workaround? Any idea where the solution might

Re: [Jmol-users] Jmol Android released

Right on...this page seems to suggest that you need to associate URLs or data types with your application in its AndroidManifest.xml file: http://stackoverflow.com/questions/2958701/launch-custom-android-application-from-android-browser Cheers, Mike --- Mike Evans Organic Chemistry Graduate Stud

Re: [Jmol-users] Jmol Android released

Downloaded! Any chance browser applets could be set up to point to the Android application if browser support for Java fails...? I'd be willing to modify code I have for existing applets, but I'm not familiar with the innards of Jmol (and especially the Android app). Cheers, Mike --- Mike Evans O

Re: [Jmol-users] 404 (Not Found) error in jmol

I run into the problem only on OS X 10.7...that may have something to do with it. Cheers, Mike On Aug 23, 2011 1:24 PM, "Jeff Hansen" wrote: > Whatever the problem is I don't think you can blame it on Safari. All three links are fine for me in Safari 5.1, OS 10.6.8. No error messages in the conso

Re: [Jmol-users] Checking for Disulfide Bonds

Sara—use the Jmol script command... select sulfur and connected(sulfur); You may be able to use the scriptCallback or messgeCallback of this command to see what was selected; what I know works is to then use show selected; to spit out selected atoms. If you get anything back, you know disulfide

Re: [Jmol-users] OT (a bit): C-I-P R/S assignments in 3D

tact the Chemaxon folks and ask if retaining the atom > labels from the mol file is possible. > > Rich > > On Jul 31, 2011, at 2:11 PM, Michael Evans wrote: > > Rich--although its 3d capabilities are not as good as jmol, marvin sketch > can do r/s assignment in 2d or 3d mol files. I

Re: [Jmol-users] OT (a bit): C-I-P R/S assignments in 3D

Rich--although its 3d capabilities are not as good as jmol, marvin sketch can do r/s assignment in 2d or 3d mol files. If that's all you're after, check out marvin sketch. http://chemaxon.com/marvin Cheers, Mike On Jul 31, 2011 1:04 PM, "Richard Ball" wrote: > > On Jul 31, 2011, at 7:11 AM, Egon

Re: [Jmol-users] Mac update

Just discovered that dragging and dropping .jmols on the applet doesn't work anymore in Lion. It opens a Finder window instead. Cheers, Mike Mike Evans Organic Chemistry Graduate Student Moore Group University of Illinois, Urbana-Champaign On Jul 22, 2011, at 12:14 PM, Michael Evans

Re: [Jmol-users] Mac update

Phil & Jmol'ers—I can add to this discussion. I've upgraded to Lion, and have experienced minimal trouble with the Java distribution recommended by Apple for downloading. It's primary downside is bad integration with the browser; if you're a Mac Chrome user you know the annoying "Java Applet" pr

[Jmol-users] Writing Would-be .jmol Contents to a Remote Location

Lords and lasses of Jmol—I am interested in writing .jmol files (really, folders containing their would-be contents) to a remote location on my server using PHP. My question is about the precise specification of .jmol. What is always included in the ZIP file, and how are the file's contents process

Re: [Jmol-users] MO HOMO/LUMO?

chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip for the fix. > I've also fixed that in Jmol 12.0, but that release will be later this week > or next week, probably. > > > ps: WebMO uses Jmol, by the way > > > 2011/6/22 Michael Evans > >> I just ref

Re: [Jmol-users] MO HOMO/LUMO?

e: > They won't work if your data does not have occupancy information. Please > check the latest version, and/or send me the offending file so I can check > it out. > > On Mon, Jun 20, 2011 at 5:53 PM, Michael Evans wrote: > >> Lords & lasses of Jmol—in several versi

Re: [Jmol-users] about charge scale legend

J—the "boundbox" command might help: http://chemapps.stolaf.edu/jmol/docs/#boundbox Boundbox bounds the entire model by default, but it shouldn't be too difficult to show only a particular side or to condense it. Try playing around with boundbox CORNERS and boundbox TICKS to achieve the desired e

[Jmol-users] MO HOMO/LUMO?

Lords & lasses of Jmol—in several versions of Jmol 12.0 (at least since .34), the "mo homo" and "mo lumo" commands don't seem to be working. The documentation seems to suggest they still should. Bug here? Could someone test this to see if I'm the only one having this issue? Cheers, Mike -- Mike

Re: [Jmol-users] simple mechanistic reaction arrows

Bob—this is *amazing*. I wrote an algorithm a while back that finds the midpoint between the start and end of an arrow and essentially "lifts" it to curve it by introducing a third intermediate point...I'm guessing that's how this works too? These look better than mine, and I will switch when they

Re: [Jmol-users] Jmol Molecular Orbital Viewer

Bob—slick tool! Maybe JmolColorPickers or some other means to change the color of MO lobes? Cheers, Mike On Thu, May 19, 2011 at 8:45 AM, Robert Hanson wrote: > I've done a bit of work on my demo page for viewing molecular orbitals and > turned it into the Jmol Molecular Orbital Viewer. > > See

Re: [Jmol-users] Java 1.5 vs 1.6 on Macs?

Eric—my laptop has Leopard, and I am running "1.5.0_28-b04." Not sure what difference the "b04" makes, but I don't experience the copy/paste problem. For the rest of the listserv, another way to see this is by simply typing "Java Preferences" into Spotlight. The version at the top of the list is th

Re: [Jmol-users] Mac Firefox Java

edu/%7Epbays/Stereochemistry.html> > > Particularly the cyclohexane options near the bottom of the list. > > > On Mar 8, 2011, at 9:49 PM, Michael Evans wrote: > > It's a little slow, but it seems to be working on my end (Snow Leopard OS > X, 10.6) on FF beta 12, based on thi

Re: [Jmol-users] Mac Firefox Java

It's a little slow, but it seems to be working on my end (Snow Leopard OS X, 10.6) on FF beta 12, based on this page: http://jmol.sourceforge.net/demo/trace/ Cheers, Mike On Tue, Mar 8, 2011 at 7:35 PM, Philip Bays wrote: > Apple released a Java security update today. It appears that Jmol now

Re: [Jmol-users] Newbie question: showing a docked receptor-ligand model (applet)

The difficulty is defining the atoms involved in the receptor...showing bonds and ribbons in the entire protein is quite easy: select protein; cartoon on; The ligand will display initially as bonds and atoms. I suspect this isn't what you want :-) Here's script for displaying bonds and atoms only

Re: [Jmol-users] molecular orbital linear combinations

Bob—a bit of a learning curve, but the jQuery UI Slider is phenomenal: http://jqueryui.com/demos/slider/ Cheers, Mike On Thu, Feb 10, 2011 at 10:00 AM, Robert Hanson wrote: > I'll check out the slider business -- does anyone know of a simple slider > widget that works universally? > > On Wed,

Re: [Jmol-users] picking atoms

Jan—here is a simple example: http://chemapps.stolaf.edu/jmol/docs/examples-11/spacegroup.htm Notice how an alert is thrown when you click on an atom. If you look at the function in the source code, "picking," that is called when an atom is clicked, you'll see how the three arguments of the funct

Re: [Jmol-users] picking atoms

Jan—you will want to play around with *set PickCallback *, which establishes a Javascript function that processes Jmol's output when an atom or group of atoms is selected. To see what exactly Jmol returns, check out the "pickCallback" section of th

Re: [Jmol-users] Connecting atoms of different models

Angel—there doesn't appear to be a way to connect atoms from different models, at least according to the documentation. I have tried loading two models, selecting one atom in each, and these commands: connect (selected); connect (selected and 1.1) (selected and 1.2); Neither results in the creati

Re: [Jmol-users] proposed default change for 12.2 CIF files

Bob—an official vote from from labmate who uses Jmol to display crystal structures for this one. Any chance it could get placed in the next release of 12.0? Cheers, Mike On Tue, Dec 7, 2010 at 8:58 AM, Robert Hanson wrote: > Brian, yes, in fact I did notice that one. Odd that the CIF doesn't in

Re: [Jmol-users] Version 12.0.24 -- important! Jmol State reading/writing!

Whew, thanks Bob! Miraculously this never caused a problem for me (that I know of), even though I had 200+ students saving state files... Cheers, Mike On Tue, Dec 7, 2010 at 9:12 AM, Robert Hanson wrote: > Jmol users, > > If you have recently upgraded to any versions Jmol 12.0.19 through 12.0.2

[Jmol-users] set picking measure...?

Is it just me, or is "set picking measure" broken in 12.0.22? When I try to measure a distance between two atoms, the measurement instantly disappears. Measuring bond and dihedral angles works fine, however. What am I missing? Cheers, Mike -- Mike Evans Organic Chemistry Graduate Student Moore G

[Jmol-users] JME/Model Kit Mode and PDBs

Hey all—I would be interested in the "write state" function working with combinations of PDB structures and inline models (built by importing from JME or via model kit mode), for docking purposes. Given the recent work that's been done on "dragminimize" and "dragminimizemolecule," it seems like a n

Re: [Jmol-users] Solid Location for Jmol's Changelog

trunk/Jmol/src/org/jmol/viewer/Jmol.properties?view=markup > > Nico > > On Mon, Nov 1, 2010 at 9:30 PM, Michael Evans wrote: > >> Lords (and lasses?) of Jmol—is there a solid location that I can bookmark >> containing the official Jmol change log? I think a problem I'm h

[Jmol-users] Solid Location for Jmol's Changelog

Lords (and lasses?) of Jmol—is there a solid location that I can bookmark containing the official Jmol change log? I think a problem I'm having is related to a bug in my current version, and (go ahead, call me lazy) I'd rather look it up to see if it's fixed in a later version than update Jmol to t

Re: [Jmol-users] default style setting

Xiao-Ping—there are *tons* of resources available! The Jmol Website - http://jmol.sourceforge.net/ The Jmol Wiki - http://wiki.jmol.org/index.php/Main_Page The Interactive Script Documentation - http://chemapps.stolaf.edu/jmol/docs/ If you can't find what you're looking for there, there's always

Re: [Jmol-users] Jmol and DSSP

Bob—consider us interested. We teach a lesson on protein secondary structures, and something like this could come in handy. Cheers, Mike On Thu, Sep 30, 2010 at 10:30 PM, Robert Hanson wrote: > Jmol users interested in protein visualization: > > Is there any interest in having Jmol be able to c

Re: [Jmol-users] Clarification of "plot ramachandran r"

e manuscript > for this... There's a PowerPoint presentation I gave on the subject at last > year's ACS meeting. See > > http://chemapps.stolaf.edu/jmol/presentations/acs2009 > > > On Mon, Sep 20, 2010 at 11:19 PM, Michael Evans wrote: > >> Bob + other Lor

[Jmol-users] Clarification of "plot ramachandran r"

Bob + other Lords of Jmol—I'm looking for some clarification of the "plot ramachandran r" specification from the Interactive Script Docs; particularly the definition of theta. It makes sense to me that theta is approximately the sum of delta phi and delta psi. I get lost with two points: - How

Re: [Jmol-users] Jmol in the Classroom

Wow, I had no idea Jmol could generate Ramachandran plots on the fly! Remarkable! On Mon, Sep 20, 2010 at 1:19 PM, Jeff Hansen wrote: > I just checked this out. I sporadically observed this behavior of zooming > instead of rotating. It didn't always happen even after loading several > structur

Re: [Jmol-users] another crash (12.0.11)

Hmm, might I suggest an orange-ish color, maybe something akin to #ffa500? Orange is about the farthest color away from the colors that already exist in that scheme right now. My second place vote goes to a deep navy blue. Now for the real reason for my e-mail: I want to make sure I understand "wr

Re: [Jmol-users] jmol downloads top 400,000

Oh man, this number is only going to grow! On Thu, Sep 2, 2010 at 2:28 PM, Robert Hanson wrote: > Just noticed that there have been over 437,000 downloads of Jmol. Wow! > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.

[Jmol-users] General Versioning Question

Lords of Jmol--I just had a quick versioning question. As Jmol 12 "blossoms" into a number of versions after its initial release, which (if any) do you advise for production usage? What's a tell-tale sign that I should switch from, say, 12.0.x to 12.1.x? Cheers, Mike -- Mike Evans Organic Chemis

Re: [Jmol-users] does someone else experience painfully slow callbacks in firefox on mac osx?

Sweet! Wonder what's different about 4.0? On Mon, Aug 16, 2010 at 4:37 PM, Alexander Rose wrote: > Hi, > > Am 16.08.2010 um 17:48 schrieb Philip Bays: > > > This seems to be another example of Mac Firefox (and I suspect Camino and > SeaMonkey) behaving differently. I would be interested in the

Re: [Jmol-users] does someone else experience painfully slow callbacks in firefox on mac osx?

Seconded. I thought this would be fixed back when the "200 ms" issue was fixed, but I'm still experiencing slow callbacks. On Mon, Aug 16, 2010 at 8:50 AM, Alexander Rose wrote: > Hi, > > does someone else experience painfully slow callbacks in firefox on mac > osx? > > http://weirdbyte.de/jmol-

Re: [Jmol-users] Problems with JVXL Files?

the actual JVXL file. > > > > > On Sun, Aug 15, 2010 at 11:11 AM, Michael Evans wrote: > >> Jmol team--I've had problems lately with JVXL files in Jmol. In Jmol >> 12.0.2, I cannot get them to load at all. Has something changed with respect >> to the file sp

[Jmol-users] Problems with JVXL Files?

Jmol team--I've had problems lately with JVXL files in Jmol. In Jmol 12.0.2, I cannot get them to load at all. Has something changed with respect to the file specification for JVXL files in Jmol 12, or could this be a bug? Here's an example of a simple applet that is supposed to load a JVXL isosurf

Re: [Jmol-users] Performance issue with setcallback useCommandThread

FYI, I run into the same problem in the Firefox version of our Jmol Interface, except using a JmolScript call in a pickCallback method. On Fri, Jul 23, 2010 at 12:52 PM, Robert Hanson wrote: > > > On Fri, Jul 23, 2010 at 9:18 AM, Paul Pillot < > paul.pil...@ac-orleans-tours.fr> wrote: > >> >> I

Re: [Jmol-users] Applet coming through dynamic iframe

Scratch that; it's not working as well as I thought. It loads the state script in the uncloaked applet, oddly enough, only after the page has been re-loaded. On Thu, Jul 22, 2010 at 11:20 AM, Michael Evans wrote: > Jmolians--I'm having an interesting problem with Jmol applets in

[Jmol-users] Applet coming through dynamic iframe

Jmolians--I'm having an interesting problem with Jmol applets in dynamically loaded iframes. https://wiki.cites.uiuc.edu/wiki/display/CHEM332Molmodac/expt In the page linked above, the applet at the very bottom of the page is displaying just fine--exactly the way I want it to, in the proper state

Re: [Jmol-users] Jmol-users Digest, Vol 50, Issue 44

a different function for the + and - > cases and update the color for each one. > > Let me know what you come up with. > > Jonathan > On Jul 20, 2010, at 5:59 AM, jmol-users-requ...@lists.sourceforge.net > wrote: > > > Date: Mon, 19 Jul 2010 16:39:39 -0500 > > From: M

[Jmol-users] Using multiple jmolColorPickers in a single command?

Is there a way to use input from two different color pickers in a single Jmol command? I'm thinking along the lines of isosurface and MO. A way to set the positive and negative colors for these commands independently would obviate the need for this feature (if it doesn't exist already), but it woul

[Jmol-users] Animations of Gaussian Geometry Optimization

Lords of Jmol: I came across an interesting question the other day. A student wants to use Gaussian .log output to build an animation of the geometry minimization process from Gaussian's point of view, with each frame corresponding to a different geometry until the optimized structure is reached. A

Re: [Jmol-users] Jmol model kit and docking

Bob--this is truly amazing! Our students just last semester were asking about docking small molecules to proteins in Jmol...this'll be interesting to explore with existing PDB structures...wonder if Jmol agrees with the crystal structures from an energetic and conformational point of view? That'd b