Re: [Jmol-users] open function not working, only for one user?

2014-02-05 Thread Angel Herráez
James, It does not make much sense to me, as you think too. I agree it should not be a Java path problem. Maybe: since Jmol is not installed, but just copied, try to check what the permissions are on the Jmol.jar file and folder. It may belong to one user and the other not have ful permissions

Re: [Jmol-users] Jsmol fails to load the pdb file in Chrome, works in Firefox

2014-02-05 Thread Robert Hanson
the .zip in the file name is almost certainly telling JSmol that this is a zip file and thus binary. Jmol/Java doesn't care, but JSmol/HTML5 does. And Chrome is the one that would be affected. So either (1) change that file signature to not include zip or (2) add a JavaScript line after you load

Re: [Jmol-users] Tinker xyz files as Jmol input

2014-02-05 Thread Robert Hanson
test files, please. have another idea. On Mon, Feb 3, 2014 at 12:10 PM, Whitwell, George gwhitw...@ncwc.eduwrote: Bob, Don't recall that you did. Tinker uses the same format for dynamics archives with multiple structures. In my test, load tinker::argon.arcread the first model (of

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

2014-02-05 Thread Robert Hanson
I will look into implementing that. Might be 1 -50 100 -51 IE minus signs. (This is an array) On Mon, Feb 3, 2014 at 12:32 AM, Rzepa, Henry S h.rz...@imperial.ac.ukwrote: On 3 Feb 2014, at 05:42, Robert Hanson hans...@stolaf.edu wrote: Henry, you can animate frames in any order now.

Re: [Jmol-users] Question: What is the preferred way to save JSmol state and orientation?

2014-02-05 Thread Robert Hanson
PNGJ is not designed to save any settings other than those that are specifically necessary to define a state. So no user variables, no overall preferences. You could save a message in the state by using the message command, I suppose, but that would have to be a message that was visible to the

[Jmol-users] Frederick Maryland power out; NCI resolver down for duration

2014-02-05 Thread Robert Hanson
There has been a severe ice storm that shut down the NCI resolver. So load $ will be out until that resolves. -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is

Re: [Jmol-users] Question: What is the preferred way to save JSmol state and orientation?

2014-02-05 Thread Charles Harrison Shubert
Hi Bob, I guess I would have been surprised if a backdoor existed. Thanks for thinking about this. —Chuck On Feb 5, 2014, at 4:45 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: PNGJ is not designed to save any settings other than those that are specifically necessary

[Jmol-users] unitcell and/or draw unitcell command changed between 13.3.3 and 14.1.6?

2014-02-05 Thread Dean Johnston
Jmol users list, I’ve noticed a change in behavior of the unitcell/draw unitcell command somewhere between 13.3.3 and 14.1.6. I’m using it to draw representations of multiple unit cells of simple crystal structures like bcc, fcc, etc. I use the unitcell and draw unitcell commands to draw

Re: [Jmol-users] unitcell and/or draw unitcell command changed between 13.3.3 and 14.1.6?

2014-02-05 Thread Robert Hanson
Looks like a bug in DRAW. I will fix it. hmm. What's this about, by the way? I hope we don't need that sort of thing. If we do, I need to fix something. var $j = jQuery.noConflict(); On Wed, Feb 5, 2014 at 5:33 PM, Dean Johnston djohnsto...@gmail.com wrote: Jmol users list, I've

Re: [Jmol-users] unitcell and/or draw unitcell command changed between 13.3.3 and 14.1.6?

2014-02-05 Thread Dean Johnston
hmm. What's this about, by the way? I hope we don't need that sort of thing. If we do, I need to fix something.       var $j = jQuery.noConflict(); I used the Prototype.js library for these pages. It uses $() syntax for DOM queries like jQuery. I’m slowly removing the dependence on

[Jmol-users] Spectra

2014-02-05 Thread Otis Rothenberger
Bob, A while back I added a Resolver down detection to our model kit. This automatically switches us over to ChemSpider smiles to inchi and PubChem loading. Doing this keeps all of our database connections open - NIST, JME to Jmol load, etc. Everything works, albeit in the context of the