[Jmol-users] selecting atoms across frames

2014-09-09 Thread Anders Østergaard Madsen
Dear Jmol users, I have loaded a file from the CRYSTAL program to Jmol. It is a file showing multiple vibrational modes of a molecular crystal. That means that I have a large range of frames, each with a particular vibrational mode. I am able to build a supercell showing several molecules, but I w

[Jmol-users] "Info" parameters z and zIndexBase

2014-09-09 Thread Angel Herráez
Dear Bob, Can you explain the difference between Info.z and Info.zIndexBase? For now, I am setting both, but would prefer to be more specific --and also complete the doc http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Info Thanks --

[Jmol-users] broken 14.2.4

2014-09-09 Thread Angel Herráez
Hi I have problems with JSmol/Html5 version 14.2.4 Both with my major pages (complex) and with a very simple test page, I get the same error on page loading with a single Jmol object: The Jmol box displays: Jmol._Canvas2D (Jmol) "myJmol"[x] Smol/j2s/core/package.js And the browser JS conso

[Jmol-users] molecular dipoles

2014-09-09 Thread Pshemak Maslak
I have run into an issue with displaying molecular dipoles (and finding their values). mol2 file (with Mulliken partial charges) will not display (or calculate) the molecular dipole. /dipole molecular/ or /dipole calculate molecular/ do nothing (no error, no display of any kind) The MEP

Re: [Jmol-users] broken 14.2.4

2014-09-09 Thread Robert Hanson
There have been 1400 downloads of that, and I just downloaded and tested it again, and it worked fine. I suspect something is wrong with your implementation, Angel. I actually do not even see how that can happen. ClazzLoader is part of the main j2sjmol part, and it is what loads package.js in the

Re: [Jmol-users] broken 14.2.4

2014-09-09 Thread Angel Herráez
> There have been 1400 downloads of that, and I just downloaded and > tested it again, and it worked fine. I suspect something is wrong Well, who knows, could be cache or anything. But it got fixed when I tried the other version. Now I am testing 14.3 (because of other problems with sync) and i

[Jmol-users] Save problems

2014-09-09 Thread pino.stricc...@libero.it
Dear Friends, after long time i am working again on my site since the school has started again in Italy. And working on JSmol is always a big work for me. I have a little problem with the option of save file. I have seen that i cannot save the file on my disk because i dont receive any option o

Re: [Jmol-users] Save problems

2014-09-09 Thread Robert Hanson
It will save the file in your downloads folder; you should see a notification of that from your browser. Did it ask you for a file name (one or more times)? Bob On Tue, Sep 9, 2014 at 12:47 PM, pino.stricc...@libero.it < pino.stricc...@libero.it> wrote: > Dear Friends, after long time i am worki

Re: [Jmol-users] selecting atoms across frames

2014-09-09 Thread Robert Hanson
The frames should all have the same atom names. So if you know one, you know them all. No symmetry operators, right? -- P1? Then if that is, say, C2: select within(molecule, C2) for example. On Tue, Sep 9, 2014 at 3:56 AM, Anders Østergaard Madsen wrote: > Dear Jmol users, > > I have loaded

Re: [Jmol-users] "Info" parameters z and zIndexBase

2014-09-09 Thread Robert Hanson
Info.z is an associative array that defines explicitly what the z-index is to be for applet-related div elements. Some subset of these: Info.z = { header:, rear:, main:, image:, front:, fileOpener:, coverImage:,