Re: [Jmol-users] FW: minimize

minimization has a maximum of 100 atoms. It's not going to work with DNA. Sorry On Mon, Sep 23, 2013 at 3:04 PM, Spinney, Richard < rspin...@chemistry.ohio-state.edu> wrote: > ** ** > > I am trying to minimize a small DNA fragment from a PDB file, but minimize > does not work. There are no

Re: [Jmol-users] difficulties encountered in switching to JSmol -- part deux

There may be a few differences like that. For now, just use Jmol.script(yourAppid, 'load DATA "mydata"\n' + yourInlineData + '\nEND "mydata" ') or give this one a try: http://chemapps.stolaf.edu/jmol/jsmol/js/Jmol2.js On Mon, Sep 23, 2013 at 3:15 PM, Grossman, Robert B wrote: > OK, I read

Re: [Jmol-users] Jmol CAPTURE command?

The unsigned applet and the JavaScript code does not include the necessary classes for this particular operation. I don't see why it can't be just an application thing. By the way, animated GIFs work nicely in PowerPoint. That may be a great point of application. However, before you get too excite

Re: [Jmol-users] Jmol CAPTURE command?

That's right. We could make it available in JSmol, but I'd rather not. These files can get VERY large (50-100MB easily), and without FileWriter API (almost no browsers supporting this yet), that would require a round-trip to a server. Besides, where would you store it on your iPad? :) Any page uti

Re: [Jmol-users] Jmol-users Digest, Vol 88, Issue 65

ps -- that can be tested using test2.htm?debugcode so that the minified files are not used. On Mon, Sep 23, 2013 at 9:45 PM, Robert Hanson wrote: > It's probably something to do with my rewrite of the jQuery extension. > I'll need more specifics. You may have to put some alerts in to see where

Re: [Jmol-users] Jmol-users Digest, Vol 88, Issue 65

It's probably something to do with my rewrite of the jQuery extension. I'll need more specifics. You may have to put some alerts in to see where the issue is Try JSmoljQueryExt.js or JSmolCore.js On Mon, Sep 23, 2013 at 12:58 AM, Geoffrey Rowland wrote: > Hi > > I may have not made myself clear

[Jmol-users] FW: minimize

I am trying to minimize a small DNA fragment from a PDB file, but minimize does not work. There are no error messages and the "computation" link in the menu is grayed out. I have missed something in the loading the file (i.e. a required set command) or does minimize not work on PDB files? I am

[Jmol-users] difficulties encountered in switching to JSmol -- part deux

OK, I read a little further down in the Wiki and saw that I could accomplish the switch another way: leave the calls to jmolApplet(), etc. alone and instead use both JSmol.min.js and Jmol2.js as resources. So I did so, and I also added a symlink to the jsmol/j2s folder in the same folder as the

Re: [Jmol-users] difficulties encountered in switching to JSmol -- advice please?

Hi Bob (Groosman) Didn't you get the reply las Friday? see http://www.mail-archive.com/jmol-users@lists.sourceforge.net/msg21780.ht ml -- October Webinars: Code for Performance Free Intel webinars can help you accelerat

[Jmol-users] difficulties encountered in switching to JSmol -- advice please?

Hi all, I am looking at switching from Jmol to JSmol. The WIki page says , Modifying function calls from the format jmolXxxx(..., appletExtension) to Jmol.jmolXxxx(appletID, ...) So I have done that, and I am seeing undefined methods errors in the error console: TypeError: 'undefined' is not

Re: [Jmol-users] Jmol CAPTURE command?

Amjad, JSmol uses the same base code and the same set of commands than Jmol. So you should be able to do it. http://www.mail-archive.com/jmol-users@lists.sourceforge.net/msg21798.ht ml -- October Webinars: Code for Perf

[Jmol-users] Fwd: Jmol-users Digest, Vol 88, Issue 60

Dear Paul and other Jmolers, Yes, I would be delighted to provide the software, and any other guidance, for setting up your own Molecular Playground. A description of the project and basic installation guidelines can be found at . My goal is to have the softwar

Re: [Jmol-users] Jmol CAPTURE command?

Bob, This new feature to produce a GIF animation is very useful. However, I assume it is only available in Jmol and not JSmol. Is that correct? If this feature is also available in JSmol, can you please remind us what the command to generate such an animation would be. Thanks! Amjad On Sun,