Re: [Jmol-users] Jmol Site

2017-01-01 Thread darren.rhodes
Nailed it. Thanks. Darren. On 1 January 2017 at 07:16, Robert Hanson wrote: > The main problem with that call was that it was an http call from an https > page. That's not allowed. Good news is that all you have to do is add the > "s": > > https://chemapps.stolaf.edu/jmol/jmol.php?source=https:

Re: [Jmol-users] Jmol Site

2016-12-31 Thread Robert Hanson
The main problem with that call was that it was an http call from an https page. That's not allowed. Good news is that all you have to do is add the "s": https://chemapps.stolaf.edu/jmol/jmol.php?source=https:// files.figshare.com/1860026/ethen_01oIRC.cml right? Bob -- Robert M. Hanson Larso

Re: [Jmol-users] Jmol Site

2016-12-31 Thread darren.rhodes
I don't have an account to the wiki ... can anyone who does have an account update it for me (us) please? One tiny thing ... the resulting webpage carries the title 'aspirin' if you have the time could you modify it, please? Thanks all Darren. On 31 December 2016 at 14:29, darren.rhodes wrote:

Re: [Jmol-users] Jmol Site

2016-12-31 Thread darren.rhodes
Hi All Found the problem ... it looks like figshare has had a re-configuration in the manner in which it serves the data that it stores. Old url ... http://chemapps.stolaf.edu/jmol/jmol.php?source=http://files.figshare.com/1860026/ethen_01oIRC.cml New url ... https://chemapps.stolaf.edu/jmol/

Re: [Jmol-users] Jmol Site

2016-12-31 Thread darren.rhodes
Hi Robert the following http://chemapps.stolaf.edu/jmol/jmol.php?source=http://files.figshare.com/1860026/ethen_01oIRC.cml crashes out again. Do you have a remedy? Yes, I cleared my cache before trying. Thanks Darren. ps the code is one of the exemplars on the wiki http://wiki.jmol.org/index

Re: [Jmol-users] Jmol Site

2015-10-19 Thread darren.rhodes
Works like a charm again. thanks Darren. On 20 October 2015 at 03:41, Robert Hanson wrote: > Thanks -- clear your cache and try again. I forgot to update a file on my > server. > > On Mon, Oct 19, 2015 at 6:59 AM, darren.rhodes > wrote: >> >> Hi Robert >> >> The charm has gone? >> >> I tried t

Re: [Jmol-users] Jmol Site

2015-10-19 Thread Robert Hanson
Thanks -- clear your cache and try again. I forgot to update a file on my server. On Mon, Oct 19, 2015 at 6:59 AM, darren.rhodes wrote: > Hi Robert > > The charm has gone? > > I tried to right click on the result of the following line of code but > I it didn't work like it did a few months ago.

Re: [Jmol-users] Jmol Site

2015-10-19 Thread darren.rhodes
Hi Robert The charm has gone? I tried to right click on the result of the following line of code but I it didn't work like it did a few months ago. http://chemapps.stolaf.edu/jmol/jmol.php?source=http://files.figshare.com/1426063/s2cl2_b_2.22cTS.log instead it throws an error. Can you suggest

Re: [Jmol-users] Jmol Site

2015-01-03 Thread Angel Herráez
Hi Darren There is some limitation in the length and complexity of the script in the url, I caanot give you details, But there are other choices you might use: 1. you can embed the script in the CML file (there are details about this in the Jmol Wiki) 2. you can maybe invoke in the url a scr

Re: [Jmol-users] Jmol Site

2015-01-03 Thread darren.rhodes
Hi Robert Been using the site and code you posted. Very useful, thanks. But ... how much scripting is it possible to do on the url? For example, consider http://chemapps.stolaf.edu/jmol/jmol.php?source=http://figshare.com/download/file/1828552&width=600&height=600 where the script &width=600&

Re: [Jmol-users] Jmol Site

2014-12-06 Thread Robert Hanson
So just to follow up on my last note: http://chemapps.stolaf.edu/jmol/jmol.php?source=http://files.figshare.com/1825432/MeOH_NMR01b.log Displays your model. That is not very interesting, though. The thing to do is, from your Jmol application, display whatever you particularly want to show your co

Re: [Jmol-users] Jmol Site

2014-12-06 Thread darren.rhodes
Thanks Robert. Simply changed the source http://chemapps.stolaf.edu/jmol/jmol.php?source=http://files.figshare.com/1426063/s2cl2_b_2.22cTS.log which worked like a charm. Darren. On 6 December 2014 at 21:51, Robert Hanson wrote: > You can use > > http://chemapps.stolaf.edu/jmol/jmol.php?source=h

Re: [Jmol-users] Jmol Site

2014-12-06 Thread Robert Hanson
You can use http://chemapps.stolaf.edu/jmol/jmol.php?source=http://introchem.chem.okstate.edu/DCICLA/jmol/molecules/II.A.1.ch3ch3.smol Where you just change the source attribute to whatever URL you want. See http://chemapps.stolaf.edu/jmol/jmol.php for details. On Fri, Dec 5, 2014 at 6:32

Re: [Jmol-users] Jmol Site

2014-12-06 Thread darren.rhodes
Hi Rolf Thanks ... that's exactly what I was hoping to find. Darren. On 6 December 2014 at 18:52, Rolf Huehne wrote: > Am 06.12.14 11:39, schrieb darren.rhodes: >> Hi Eric >> >> Thanks for your reply ... I'll look at Proteopedia. In the mean time >> here's some clarification. >> >> When I

Re: [Jmol-users] Jmol Site

2014-12-06 Thread Rolf Huehne
Am 06.12.14 11:39, schrieb darren.rhodes: > Hi Eric > > Thanks for your reply ... I'll look at Proteopedia. In the mean time > here's some clarification. > > When I type the following on my command line, > > jmol MeOH_NMR01b.log & > > As is common to our shared experience, jmol starts up, the str

Re: [Jmol-users] Jmol Site

2014-12-06 Thread Angel Herráez
Eric, I agree with you but --as I understand it-- Darren does not want to edit pages (one per model). There is also a concern regarding uploading his files to Proteopedia -- they have nothing to do with biomolecules, and he is not interested in writing descriptions about them, I think. He just

Re: [Jmol-users] Jmol Site

2014-12-06 Thread Eric Martz
All 3 issues raised by Angel below are eliminated if you use Proteopedia. Again, let me know if you'd like help or an example -- or Angel can help as he is also familiar with Proteopedia. On 12/6/14 7:48 AM, Angel Herráez wrote: > Caveats: > > 1. Such a cross-origin file request may fail dependi

Re: [Jmol-users] Jmol Site

2014-12-06 Thread Rzepa, Henry S
> On 6 Dec 2014, at 12:48, Angel Herráez wrote: > > Darren, I've done a test locally, and it is indeed possible to display the > model > loaded from figshare (using the download URL, not the page URL) in a > JSmol page. > > i.e. http://files.figshare.com/1825432/MeOH_NMR01b.log > > The link

Re: [Jmol-users] Jmol Site

2014-12-06 Thread darren.rhodes
Thanks for your help (and also the help of the others who contributed to the thread). Darren. On 6 December 2014 at 12:48, Angel Herráez wrote: > Darren, I've done a test locally, and it is indeed possible to display the > model > loaded from figshare (using the download URL, not the page URL)

Re: [Jmol-users] Jmol Site

2014-12-06 Thread Angel Herráez
Darren, I've done a test locally, and it is indeed possible to display the model loaded from figshare (using the download URL, not the page URL) in a JSmol page. i.e. http://files.figshare.com/1825432/MeOH_NMR01b.log The link you could share with collaborators is of the form http://some.server

Re: [Jmol-users] Jmol Site

2014-12-06 Thread Angel Herráez
darren.rhodes wrote: > Hi Angel > > Thanks for your note but I was hoping to be able to exhibit the full > flavour of a GAMESS (US) log file Yes, that was clear. I mentioned SMILES just because it works but I was anticipating it was not your case. -

Re: [Jmol-users] Jmol Site

2014-12-06 Thread Angel Herráez
darren.rhodes wrote: > When I type the following on my command line, > > jmol MeOH_NMR01b.log & > > As is common to our shared experience, jmol starts up, the structure > found within the file MeOH_NMR.log is appears and it can be > interrogated using the tools that ship with jmol. Yes, but tha

Re: [Jmol-users] Jmol Site

2014-12-06 Thread darren.rhodes
Hi Angel Thanks for your note but I was hoping to be able to exhibit the full flavour of a GAMESS (US) log file, for example, I've got an IRC of a dehyrdation reaction which I'd like to be able to share with not only the cognescenti (those on this group) but the non-cognescenti (intelligent and ca

Re: [Jmol-users] Jmol Site

2014-12-06 Thread darren.rhodes
Hi Eric Thanks for your reply ... I'll look at Proteopedia. In the mean time here's some clarification. When I type the following on my command line, jmol MeOH_NMR01b.log & As is common to our shared experience, jmol starts up, the structure found within the file MeOH_NMR.log is appears and i

Re: [Jmol-users] Jmol Site

2014-12-06 Thread Nina Jeliazkova
On 6 December 2014 at 12:26, Angel Herráez wrote: > Hi Darren > > There are two issues in your question > 1. where to locate the page that holds Jmol (I have understood you do not > want to create it) > 2. where to locate the data file > > There is something similar implemented, e.g. in Wikipedia

Re: [Jmol-users] Jmol Site

2014-12-06 Thread Angel Herráez
Hi Darren There are two issues in your question 1. where to locate the page that holds Jmol (I have understood you do not want to create it) 2. where to locate the data file There is something similar implemented, e.g. in Wikipedia. Many molecules, like https://en.wikipedia.org/wiki/Citrate ha

Re: [Jmol-users] Jmol Site

2014-12-05 Thread Rzepa, Henry S
> On 6 Dec 2014, at 04:37, Eric Martz wrote: > > Dear Darren, > > I'm not sure that I understand what you want, but you can show any structure > in JSmol at Proteopedia.org, in a web page that anyone can access. The data > file(s) can be uploaded to the server and used for that showing, and y

Re: [Jmol-users] Jmol Site

2014-12-05 Thread Rzepa, Henry S
We have a demo (and a journal article) coming up at the conference FORCE2015 in January where we present a solution to this problem based on three different standards-based solutions using metadata and a persistent time-stamped identifier (DOI) assigned to the file(set). See http://doi.org/100

Re: [Jmol-users] Jmol Site

2014-12-05 Thread Eric Martz
Dear Darren, I'm not sure that I understand what you want, but you can show any structure in JSmol at Proteopedia.org, in a web page that anyone can access. The data file(s) can be uploaded to the server and used for that showing, and you can put links in the web page that would allow any vis

[Jmol-users] Jmol Site

2014-12-05 Thread darren.rhodes
Is there a site where I can post a link to a structure - I'm thinking of a GAMESS (US) log file - which would return the jmol object of the structure in the file? That is, say I want to share a file with a broader audience, rather than building and hosting a web page, is there a web page out there