jmol-developers — Detailed discussions about the source code by and for Jmol developers

Re: [Jmol-developers] How to display orbitals from .cub files in JSmol

[Robert H. <ha...@st...>]

Thinking maybe the problem here is the distinction between the MO command
and the ISOSURFACE command.

The MO command is used to read basis function information from
computational output files, using this to create a molecular orbital
without the need for a huge grid-based CUBE file.

The ISOSURFACE command can do that, too, but in addition it can read volume
data from a variety of formats (including .cub files) and then create an
isosurface from that.

The ISOSURFACE command can also be the basis for creating JVXL files --
highly compressed (>200:1) single-cutoff surfaces that can be used instead
of re-reading or downloading .cub files.

In this particular case, the file was loaded using

ISOSURACE SIGN "tr.cub"

with no problem. (SIGN being the option indicating that this volume data
has both positive and negative components -- p orbitals, for example -- and
that the implied or explicit cutoff is to be used for both signs.)

BTW, I have to say that this AI summary is right on target:

GOOGLE: Jmol JVXL files

*AI Overview*
[image: Jmol and WordPress: Loading 3D molecular models, molecular ...]
JVXL files, a Jmol-specific format, store and display isosurface data, such
as molecular orbitals or electrostatic potentials, in a compressed format
for faster loading compared to large data files like CUBE files. To create
a JVXL file, you load a molecule in Jmol, use an "isosurface" command to
calculate a surface, and then use the "write isosurface filename.jvxl"
command to save the surface in the JVXL format. These smaller,
pre-calculated files are ideal for embedding on web pages using the Jmol
applet for quick display of molecular surfaces.
What are JVXL files?

   - *Purpose:* They are a proprietary format for storing isosurface data
   generated from Jmol calculations, like molecular orbitals or electrostatic
   potentials.


   -

How to create a JVXL file:

   1. *1. * *Load a molecule:*
   Open Jmol and load your desired molecular structure file (e.g., a PDB or
   MOL file).
   2. *2. * *Select a region:*
   Use the "select" command to choose the part of the molecule you want to
   generate a surface for.
   3. *3. * *Calculate the surface:*
   Use a Jmol "isosurface" command to calculate the desired surface (e.g.,
   for a molecular orbital).
   4. *4. * *Write the JVXL file:*
   Use the command write isosurface filename.jvxl to save the calculated
   surface to a JVXL file. The file will be saved to your Jmol applet
   directory.

How to use JVXL files:

   - *Loading:*
   You can load a pre-generated JVXL file using the command 'isosurface
   "filename.jvxl"' to quickly display the surface in the Jmol applet.

-
- *Format:* JVXL stands for "Jmol Voxel" and stores the data in a highly
compressed way, making it much smaller and faster to load than the
original, complete data sets (like CUBE files).
-
- *Uniqueness:* Jmol is the only application currently capable of creating
JVXL files.
-
- *Web integration:*
Copy the generated JVXL file to your web page's directory so that the path
can be easily linked within the Jmol applet, enabling faster interactive
molecule viewers for users

ref: [
https://chemapps.stolaf.edu/jmol/docs/misc/JVXL-format.pdf#:~:text=The%20Jmol%20applet%20can%20read%20and%20write,can%20be%20used%20to%20create%20JVXL%20files
.]

The only debatable term is "proprietary" there. It may be unique or
original to Jmol, but it's not "owned" by anyone. It is open source and
fully described.

Bob

Re: [Jmol-developers] How to display orbitals from .cub files in JSmol

[Rutjes, M.R. (Max) <m.r...@st...>]

This is the file that I’m trying to get work [​cub icon]  medium%SFO_A1%3 (1).cub<https://vunl-my.sharepoint.com/:u:/g/personal/m_r_rutjes_student_vu_nl/EeFuF-4tR7BCr8ZBA2RgmxoBkyZEUxx-lMLIgb87XSPVgg> However, if I would be able to use an adf.rkf file as the input for the jsmol application, from which I could visualize the orbitals would also be good, but currently only .out files work generated by ams adf, which does not contain the orbital or SFO information.

Max Rutjes

From: Robert Hanson via Jmol-developers <jmo...@li...>
Date: Wednesday, 3 September 2025 at 12:41
To: Jmol Developers <jmo...@li...>
Cc: Robert Hanson <ha...@st...>
Subject: Re: [Jmol-developers] How to display orbitals from .cub files in JSmol
Jmol users list would be better. But this is ok. Please send me the file or a link to it so I can see the issue.

Bob Hanson

Robert M. Hanson
Professor of Chemistry, Emeritus
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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

We stand on the homelands of the Wahpekute Band of the Dakota Nation. We honor with gratitude the people who have stewarded the land throughout the generations and their ongoing contributions to this region. We acknowledge the ongoing injustices that we have committed against the Dakota Nation, and we wish to interrupt this legacy, beginning with acts of healing and honest storytelling about this place.

On Tue, Sep 2, 2025, 3:19 PM Rutjes, M.R. (Max) via Jmol-developers <jmo...@li...<mailto:jmo...@li...>> wrote:

Dear Jmol developers,

I am trying to visualize molecular orbitals in JSmol using .cub files generated by ADF. When I load the file, the console shows the header line, but no orbital is displayed, while the system itself is successfully displayed.

After trying several commands, I could not get the MO to display. Could you point me in the right direction on how to visualize the MO from a .cub file? Or is there perhaps a better approach within JSmol to visualize orbitals generated with ADF?

Thank you in advance for your help.

Best regards,
Max Rutjes
_______________________________________________
Jmol-developers mailing list
Jmo...@li...<mailto:Jmo...@li...>
https://lists.sourceforge.net/lists/listinfo/jmol-developers

Re: [Jmol-developers] How to display orbitals from .cub files in JSmol

[Robert H. <ha...@st...>]

Jmol users list would be better. But this is ok. Please send me the file or
a link to it so I can see the issue.

Bob Hanson

Robert M. Hanson
Professor of Chemistry, Emeritus
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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

*We stand on the homelands of the Wahpekute Band of the Dakota Nation. We
honor with gratitude the people who have stewarded the land throughout the
generations and their ongoing contributions to this region. We acknowledge
the ongoing injustices that we have committed against the Dakota Nation,
and we wish to interrupt this legacy, beginning with acts of healing and
honest storytelling about this place.*

On Tue, Sep 2, 2025, 3:19 PM Rutjes, M.R. (Max) via Jmol-developers <
jmo...@li...> wrote:

> Dear Jmol developers,
>
> I am trying to visualize molecular orbitals in JSmol using .cub files
> generated by ADF. When I load the file, the console shows the header line,
> but no orbital is displayed, while the system itself is successfully
> displayed.
>
> After trying several commands, I could not get the MO to display. Could
> you point me in the right direction on how to visualize the MO from a
> .cub file? Or is there perhaps a better approach within JSmol to
> visualize orbitals generated with ADF?
>
> Thank you in advance for your help.
>
> Best regards,
> Max Rutjes
> _______________________________________________
> Jmol-developers mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>

[Jmol-developers] How to display orbitals from .cub files in JSmol

[Rutjes, M.R. (Max) <m.r...@st...>]

Dear Jmol developers,

I am trying to visualize molecular orbitals in JSmol using .cub files generated by ADF. When I load the file, the console shows the header line, but no orbital is displayed, while the system itself is successfully displayed.

After trying several commands, I could not get the MO to display. Could you point me in the right direction on how to visualize the MO from a .cub file? Or is there perhaps a better approach within JSmol to visualize orbitals generated with ADF?

Thank you in advance for your help.

Best regards,
Max Rutjes

[Jmol-developers] jmol can not read output file from MOPAC

[Miroslav I. <mir...@gm...>]

Hello,

attached are input and output files from MOPAC.

Jmol (the newest version) does not open input (mol) nor  out (output) file
from MOPAC...It shows "zapped".

What is please wrong with this Jmol functionality ?

Best, Miro

Re: [Jmol-developers] incorrect JSmol_spinner.gif file in distribution

[Robert H. <ha...@st...>]

Thanks, Angel. How strange. I will thank this down.

[Jmol-developers] incorrect JSmol_spinner.gif file in distribution

[Angel H. <ang...@ua...>]

Bob,
in recent releases the "JSmol_spinner.gif" image that was initially displayed at the center of the panel has been replaced with a copy of "cursor_wait.gif" that is reguularly used at bottom-left while new components are being loaded.

I see in   jsmol.zip/jsmol/j2s/img    the two files but they are identical.
While in   jsmol.zip/jsmol/img   there is the correct   JSmol_spinner.gif



 Dr. Angel Herráez
 Biochemistry and Molecular Biology,
 Dept. of Systems Biology, University of Alcalá
 E-28805 Alcalá de Henares  (Madrid), Spain

Re: [Jmol-developers] Any ideas on why I am getting the following compilation error?

[Robert H. <ha...@st...>]

Make sure your project level Java version is set to 1.8

On Sun, Dec 22, 2024, 3:22 PM Jonathan Gutow via Jmol-developers <
jmo...@li...> wrote:

> I just made a clean fork of https://github.com/BobHanson/Jmol-SwingJS
> <https://github.com/BobHanson/Jmol-SwingJS>
> BobHanson/Jmol-SwingJS: SwingJS-compatible Jmol/JSmol for Java and
> JavaScript molecular visualization and analysis - GitHub
> <https://github.com/BobHanson/Jmol-SwingJS>
> SwingJS-compatible Jmol/JSmol for Java and JavaScript molecular
> visualization and analysis - GitHub - BobHanson/Jmol-SwingJS:
> SwingJS-compatible Jmol/JSmol for Java and JavaScript molecular
> visualization and analysis
> github.com
> in a pristine copy of the latest Eclipse. When I try to run the compile of
> the Jmol.jar using the main build.xml, I get the following error:
>
>    [*javac*]
> */home/jonathan/GIT/Jmol-SwingJS/src/org/jmol/applet/Jmol.java*:303:
> error: cannot find symbol
>    [*javac*]           jsoWindow = JSObject.getWindow(applet);
>    [*javac*]                               ^
>    [*javac*]   symbol:   method getWindow(JApplet)
>    [*javac*]   location: class JSObject
>
> I am assuming I have some flag set wrong. I am running under OpenJDK 21.05
> for the Eclipse installation.
> It appears to have JavaSE 1.8 available for the build. I can run Jmol
> within Eclipse and it appears to work fine.
>
> Any thoughts?
>
> I am trying to get this working in the hopes of generating an automated
> tool chain to do:
> Jmol -> JSmol -> up-to-date npm repository that can then be plugged into a
> jupyter extension that would use
> the latest JSmol. This would be a lot easier than having to download the
> latest .zip and extract the JSmol portion.
>
> Thanks,
> Jonathan
>
>
> Dr. Jonathan Gutow
> Halsey Room 412
> Chemistry Department
> UW Oshkosh
> web: https://cms.gutow.uwosh.edu/Gutow <https://cms.uwosh.edu/G>
> e-mail: gu...@uw...
> Ph: 920-424-1326
>
> _______________________________________________
> Jmol-developers mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>

[Jmol-developers] Any ideas on why I am getting the following compilation error?

[Jonathan G. <gu...@uw...>]

I just made a clean fork of https://github.com/BobHanson/Jmol-SwingJS
[https://opengraph.githubassets.com/f599d35df30dba101347070b262f4f191f597b10a41fa2f0230c043b873b0b54/BobHanson/Jmol-SwingJS]<https://github.com/BobHanson/Jmol-SwingJS>
BobHanson/Jmol-SwingJS: SwingJS-compatible Jmol/JSmol for Java and JavaScript molecular visualization and analysis - GitHub<https://github.com/BobHanson/Jmol-SwingJS>
SwingJS-compatible Jmol/JSmol for Java and JavaScript molecular visualization and analysis - GitHub - BobHanson/Jmol-SwingJS: SwingJS-compatible Jmol/JSmol for Java and JavaScript molecular visualization and analysis
github.com
in a pristine copy of the latest Eclipse. When I try to run the compile of the Jmol.jar using the main build.xml, I get the following error:

   [javac] /home/jonathan/GIT/Jmol-SwingJS/src/org/jmol/applet/Jmol.java:303: error: cannot find symbol
   [javac]           jsoWindow = JSObject.getWindow(applet);
   [javac]                               ^
   [javac]   symbol:   method getWindow(JApplet)
   [javac]   location: class JSObject

I am assuming I have some flag set wrong. I am running under OpenJDK 21.05 for the Eclipse installation.
It appears to have JavaSE 1.8 available for the build. I can run Jmol within Eclipse and it appears to work fine.

Any thoughts?

I am trying to get this working in the hopes of generating an automated tool chain to do:
Jmol -> JSmol -> up-to-date npm repository that can then be plugged into a jupyter extension that would use
the latest JSmol. This would be a lot easier than having to download the latest .zip and extract the JSmol portion.

Thanks,
Jonathan


Dr. Jonathan Gutow
Halsey Room 412
Chemistry Department
UW Oshkosh
web: https://cms.gutow.uwosh.edu/Gutow<https://cms.uwosh.edu/G>
e-mail: gu...@uw...
Ph: 920-424-1326

Re: [Jmol-developers] JMol can not read files from Windows-WSL directories

[Robert H. <ha...@st...>]

See
https://sourceforge.net/projects/jmol/files/Jmol/Version%2016.3/Jmol%2016.3.5/

Bob

Re: [Jmol-developers] JMol can not read files from Windows-WSL directories

[Robert H. <ha...@st...>]

Miro,

I did a quick Windows WSL installation. (SO EASY!) I finally have easy
access to a Linux box just from the new Windows command line interface.
Fantastic! Finally Windows has made this easy.

The following work already in Jmol 16.3.3:

load "file://wsl$/Ubuntu/home/hansonr/t2.mol"
write "//wsl$/Ubuntu/home/hansonr/t.mol"

note the forward slashes and the use of "file:" only for load, not write.

The only reason "file:" is needed is that Jmol isn't recognizing the
\\wsl$\ prefix as a root directory in the current version. But this is
fixed for Jmol 16.3.5.

So in this coming version, those still work, and all of these work:

load  \\wsl$\Ubuntu\home\hansonr\t2.mol
load  "\\\\wsl$\\Ubuntu\\home\\hansonr\\t2.mol"
load "//wsl$/Ubuntu/home/hansonr/t2.mol"
load file://wsl$/Ubuntu/home/hansonr/t2.mol
load "file://wsl$/Ubuntu/home/hansonr/t2.mol"

write  \\wsl$\Ubuntu\home\hansonr\t.mol
write  "\\\\wsl$\\Ubuntu\\home\\hansonr\\t.mol"
write "//wsl$/Ubuntu/home/hansonr/t.mol"
write file://wsl$/Ubuntu/home/hansonr/t.mol
write "file://wsl$/Ubuntu/home/hansonr/t.mol"

Note that in each case, the file name starts with two forward or two
backward slashes.

Quotation marks are recommended. They aren't needed here because of the
particular command options and file name given.


Bob

Re: [Jmol-developers] JMol can not read files from Windows-WSL directories

[Robert H. <ha...@st...>]

Mirosolav,

Try adding

\\wsl$

And see if that works.

Try this as

\wsl$\

or other combinations of one or two back slashes and let me know what you
discover.

If in quotes the \\ will represent only one slash.

Bob

Re: [Jmol-developers] JMol can not read files from Windows-WSL directories

[Robert H. <ha...@st...>]

Q. Is this Jmol running on the Windows side? Reading files from the Linux
partition?

Try adding file: to the start of your path. This should work for loading at
least.

But do you also need to write?



On Sun, Nov 10, 2024, 12:54 PM Miroslav Iliaš <mir...@gm...> wrote:

> Hello,
>
> there is the WSL Linux emulator under Windows (
> https://learn.microsoft.com/en-us/windows/wsl/about), with its
> own filesystem.
>
> The problem is that WSL file paths are of the form
> *\\wsl.localhost\Ubuntu\home*
> \miroi\work\projects\cvicenia-z-molekulave-modelovanie\kofein
>
> so JMol and some other Windows programs can not read files from such paths.
>
> [image: image.png]
>
> Please, make a fix.
>
> Thanks,
>
> Miro
>
>
> _______________________________________________
> Jmol-developers mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>

Re: [Jmol-developers] JMol can not read files from Windows-WSL directories

[Robert H. <ha...@st...>]

I see, so two \\ means "top level". I will check into this.

On Sun, Nov 10, 2024 at 12:54 PM Miroslav Iliaš <mir...@gm...>
wrote:

> Hello,
>
> there is the WSL Linux emulator under Windows (
> https://learn.microsoft.com/en-us/windows/wsl/about), with its
> own filesystem.
>
> The problem is that WSL file paths are of the form
> *\\wsl.localhost\Ubuntu\home*
> \miroi\work\projects\cvicenia-z-molekulave-modelovanie\kofein
>
> so JMol and some other Windows programs can not read files from such paths.
>
> [image: image.png]
>
> Please, make a fix.
>
> Thanks,
>
> Miro
>
>
> _______________________________________________
> Jmol-developers mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>


-- 
Robert M. Hanson
Professor of Chemistry, Emeritus
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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

*We stand on the homelands of the Wahpekute Band of the Dakota Nation. We
honor with gratitude the people who have stewarded the land throughout the
generations and their ongoing contributions to this region. We acknowledge
the ongoing injustices that we have committed against the Dakota Nation,
and we wish to interrupt this legacy, beginning with acts of healing and
honest storytelling about this place.*

[Jmol-developers] JMol can not read files from Windows-WSL directories

[Miroslav I. <mir...@gm...>]

Hello,

there is the WSL Linux emulator under Windows (
https://learn.microsoft.com/en-us/windows/wsl/about), with its
own filesystem.

The problem is that WSL file paths are of the form
*\\wsl.localhost\Ubuntu\home*
\miroi\work\projects\cvicenia-z-molekulave-modelovanie\kofein

so JMol and some other Windows programs can not read files from such paths.

[image: image.png]

Please, make a fix.

Thanks,

Miro

Re: [Jmol-developers] jmol.org still without https

[Miguel H. <mi...@jm...>]

Ok, I'll look into it.

On Wed, Jun 12, 2024 at 6:41 AM Robert Hanson <ha...@st...> wrote:

> I don't know what that involves
>
> On Sun, Jun 9, 2024, 11:22 AM Miguel Howard <mi...@jm...> wrote:
>
>> I *think* this is what needs to happen …
>>
>> Bob,
>>
>> Pls resubmit AWS request to renew SSL cert for *.jmol.org and I will
>> approve.
>>
>> Cert then gets sent to Jaime (?) to install on wiki.
>>
>>
>> Miguel
>>
>> On Sun, Jun 9, 2024 at 05:15 Egon Willighagen <ego...@gm...>
>> wrote:
>>
>>>
>>> Hi all,
>>>
>>> what's the state of this? I saw a test email and jmol.org seems to be
>>> working for me, but wiki.jmol.org is not yet.
>>>
>>> Anything I can do to help?
>>>
>>> Egon
>>>
>>> On Fri, 31 May 2024 at 18:28, Angel Herráez <ang...@ua...>
>>> wrote:
>>>
>>>> Hello
>>>>
>>>> I believe it is Miguel who must deal with solving this.
>>>>
>>>> Jaime has checked the status at Amazon Web Server and this is his
>>>> report:
>>>>
>>>> It has happened the same as last time (last year?): renewal of the SSL certificate for wiki.jmol.org : AWS emails the owner of the domain jmol.org requesting a reply. It has not happened. A resending of the email has just been requested.
>>>>
>>>> There are 2 separate domains: jmol.org & *.jmol.org, a separate email warning will be generated for each one.
>>>>
>>>> Target email addresses are ad...@jm..., adm...@jm..., hos...@jm..., pos...@jm..., web...@jm...
>>>>
>>>> Can we have this sorted out, Miguel?
>>>>
>>>> ·
>>>>  Dr. Angel Herráez
>>>>  Biochemistry and Molecular Biology,
>>>>  Dept. of Systems Biology, University of Alcalá
>>>>  E-28805 Alcalá de Henares  (Madrid), Spain
>>>>  https://biomodel.uah.es/
>>>>
>>>> _______________________________________________
>>>> Jmol-developers mailing list
>>>> Jmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>>
>>>
>>>>
>>>
>>> --
>>> Some nanomaterials stress our cells and cause key event, some towards
>>> adverse outcomes. Read about it in our new paper "From papers to RDF-based
>>> integration of physicochemical data and adverse outcome pathways for
>>> nanomaterials", https://doi.org/10.1186/s13321-024-00833
>>>
>>> --
>>> E.L. Willighagen
>>> Department of Bioinformatics - BiGCaT
>>> Maastricht University (http://www.bigcat.unimaas.nl/)
>>> Blog: https://chem-bla-ics.linkedchemistry.info/
>>> Mastodon: https://social.edu.nl/@egonw
>>> PubList: https://orcid.org/0000-0001-7542-0286
>>>
>>

Re: [Jmol-developers] jmol.org still without https

[Robert H. <ha...@st...>]

I don't know what that involves

On Sun, Jun 9, 2024, 11:22 AM Miguel Howard <mi...@jm...> wrote:

> I *think* this is what needs to happen …
>
> Bob,
>
> Pls resubmit AWS request to renew SSL cert for *.jmol.org and I will
> approve.
>
> Cert then gets sent to Jaime (?) to install on wiki.
>
>
> Miguel
>
> On Sun, Jun 9, 2024 at 05:15 Egon Willighagen <ego...@gm...>
> wrote:
>
>>
>> Hi all,
>>
>> what's the state of this? I saw a test email and jmol.org seems to be
>> working for me, but wiki.jmol.org is not yet.
>>
>> Anything I can do to help?
>>
>> Egon
>>
>> On Fri, 31 May 2024 at 18:28, Angel Herráez <ang...@ua...> wrote:
>>
>>> Hello
>>>
>>> I believe it is Miguel who must deal with solving this.
>>>
>>> Jaime has checked the status at Amazon Web Server and this is his report:
>>>
>>> It has happened the same as last time (last year?): renewal of the SSL certificate for wiki.jmol.org : AWS emails the owner of the domain jmol.org requesting a reply. It has not happened. A resending of the email has just been requested.
>>>
>>> There are 2 separate domains: jmol.org & *.jmol.org, a separate email warning will be generated for each one.
>>>
>>> Target email addresses are ad...@jm..., adm...@jm..., hos...@jm..., pos...@jm..., web...@jm...
>>>
>>> Can we have this sorted out, Miguel?
>>>
>>> ·
>>>  Dr. Angel Herráez
>>>  Biochemistry and Molecular Biology,
>>>  Dept. of Systems Biology, University of Alcalá
>>>  E-28805 Alcalá de Henares  (Madrid), Spain
>>>  https://biomodel.uah.es/
>>>
>>> _______________________________________________
>>> Jmol-developers mailing list
>>> Jmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>
>>
>>>
>>
>> --
>> Some nanomaterials stress our cells and cause key event, some towards
>> adverse outcomes. Read about it in our new paper "From papers to RDF-based
>> integration of physicochemical data and adverse outcome pathways for
>> nanomaterials", https://doi.org/10.1186/s13321-024-00833
>>
>> --
>> E.L. Willighagen
>> Department of Bioinformatics - BiGCaT
>> Maastricht University (http://www.bigcat.unimaas.nl/)
>> Blog: https://chem-bla-ics.linkedchemistry.info/
>> Mastodon: https://social.edu.nl/@egonw
>> PubList: https://orcid.org/0000-0001-7542-0286
>>
>

Re: [Jmol-developers] jmol.org still without https

[Miguel H. <mi...@jm...>]

I *think* this is what needs to happen …

Bob,

Pls resubmit AWS request to renew SSL cert for *.jmol.org and I will
approve.

Cert then gets sent to Jaime (?) to install on wiki.


Miguel

On Sun, Jun 9, 2024 at 05:15 Egon Willighagen <ego...@gm...>
wrote:

>
> Hi all,
>
> what's the state of this? I saw a test email and jmol.org seems to be
> working for me, but wiki.jmol.org is not yet.
>
> Anything I can do to help?
>
> Egon
>
> On Fri, 31 May 2024 at 18:28, Angel Herráez <ang...@ua...> wrote:
>
>> Hello
>>
>> I believe it is Miguel who must deal with solving this.
>>
>> Jaime has checked the status at Amazon Web Server and this is his report:
>>
>> It has happened the same as last time (last year?): renewal of the SSL certificate for wiki.jmol.org : AWS emails the owner of the domain jmol.org requesting a reply. It has not happened. A resending of the email has just been requested.
>>
>> There are 2 separate domains: jmol.org & *.jmol.org, a separate email warning will be generated for each one.
>>
>> Target email addresses are ad...@jm..., adm...@jm..., hos...@jm..., pos...@jm..., web...@jm...
>>
>> Can we have this sorted out, Miguel?
>>
>> ·
>>  Dr. Angel Herráez
>>  Biochemistry and Molecular Biology,
>>  Dept. of Systems Biology, University of Alcalá
>>  E-28805 Alcalá de Henares  (Madrid), Spain
>>  https://biomodel.uah.es/
>>
>> _______________________________________________
>> Jmol-developers mailing list
>> Jmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>
>>
>
> --
> Some nanomaterials stress our cells and cause key event, some towards
> adverse outcomes. Read about it in our new paper "From papers to RDF-based
> integration of physicochemical data and adverse outcome pathways for
> nanomaterials", https://doi.org/10.1186/s13321-024-00833
>
> --
> E.L. Willighagen
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Blog: https://chem-bla-ics.linkedchemistry.info/
> Mastodon: https://social.edu.nl/@egonw
> PubList: https://orcid.org/0000-0001-7542-0286
>

Re: [Jmol-developers] jmol.org still without https

[Egon W. <ego...@gm...>]

Hi all,

what's the state of this? I saw a test email and jmol.org seems to be
working for me, but wiki.jmol.org is not yet.

Anything I can do to help?

Egon

On Fri, 31 May 2024 at 18:28, Angel Herráez <ang...@ua...> wrote:

> Hello
>
> I believe it is Miguel who must deal with solving this.
>
> Jaime has checked the status at Amazon Web Server and this is his report:
>
> It has happened the same as last time (last year?): renewal of the SSL certificate for wiki.jmol.org : AWS emails the owner of the domain jmol.org requesting a reply. It has not happened. A resending of the email has just been requested.
>
> There are 2 separate domains: jmol.org & *.jmol.org, a separate email warning will be generated for each one.
>
> Target email addresses are ad...@jm..., adm...@jm..., hos...@jm..., pos...@jm..., web...@jm...
>
> Can we have this sorted out, Miguel?
>
> ·
>  Dr. Angel Herráez
>  Biochemistry and Molecular Biology,
>  Dept. of Systems Biology, University of Alcalá
>  E-28805 Alcalá de Henares  (Madrid), Spain
>  https://biomodel.uah.es/
>
> _______________________________________________
> Jmol-developers mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>


-- 
Some nanomaterials stress our cells and cause key event, some towards
adverse outcomes. Read about it in our new paper "From papers to RDF-based
integration of physicochemical data and adverse outcome pathways for
nanomaterials", https://doi.org/10.1186/s13321-024-00833

--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Blog: https://chem-bla-ics.linkedchemistry.info/
Mastodon: https://social.edu.nl/@egonw
PubList: https://orcid.org/0000-0001-7542-0286

[Jmol-developers] test from miguel@jmol.org take 2

[Miguel H. <mi...@jm...>]

test from mi...@jm... take 2

Re: [Jmol-developers] jmol.org still without https

[Angel H. <ang...@ua...>]

Hello

I believe it is Miguel who must deal with solving this.

Jaime has checked the status at Amazon Web Server and this is his report:

It has happened the same as last time (last year?): renewal of the SSL certificate for wiki.jmol.org : AWS emails the owner of the domain jmol.org requesting a reply. It has not happened. A resending of the email has just been requested.

There are 2 separate domains: jmol.org & *.jmol.org, a separate email warning will be generated for each one.

Target email addresses are...@jm...,adm...@jm...,hos...@jm...,pos...@jm...,web...@jm...  

Can we have this sorted out, Miguel?

·
  Dr. Angel Herráez
  Biochemistry and Molecular Biology,
  Dept. of Systems Biology, University of Alcalá
  E-28805 Alcalá de Henares  (Madrid), Spain
  https://biomodel.uah.es/

[Jmol-developers] jmol.org still without https

[Angel H. <ang...@ua...>]

jmol.org domain is still without https access (SSL certificate expired)

http://jmol.org redirects to  https://jmol.sourceforge.net/   but e.g.  wiki.jmol.org  (hosted in Amazon Web Services courtesy of Jaime) uses no redirection and is displayed as insecure.

Can we sort out what the situation is, and how to renew the certificate?


 Dr. Angel Herráez
 Biochemistry and Molecular Biology,
 Dept. of Systems Biology, University of Alcalá
 E-28805 Alcalá de Henares  (Madrid), Spain

[Jmol-developers] expired certificate

[Angel H. <ang...@ua...>]

It seems that the SSH certificate for (https)  jmol.org has expired today

I assume this is in the hands of Miguel -- Is that right?

Do we need to make a collect?  ;-)

·
  Dr. Angel Herráez
  Biochemistry and Molecular Biology,
  Dept. of Systems Biology, University of Alcalá
  E-28805 Alcalá de Henares  (Madrid), Spain
  https://biomodel.uah.es/

Re: [Jmol-developers] localization missing in 16.1.53

[Angel H. <ang...@ua...>]

Good! and cleaner too regarding web server setup of files
[cid:2a91fb5e-98dc-4b09-9301-920922c4dd25]

Re: [Jmol-developers] localization missing in 16.1.53

[Robert H. <ha...@st...>]

Angel, you can try it here:

https://chemapps.stolaf.edu/jmol/jsmol/jsmol/htm

Maybe clear your browser cache. It was a simple fix -- just needed to
adjust a bit of code in org.jmol.i18n.Resource so that JSmol no longer gets
the .po files from that special idioma directory.
Both Java and JavaScript now handle localization the same way. The files
are in j2s/J/translation/JmolApplet.
Thanks again for spotting this.

Bob