jmol-developers Mailing List for Jmol

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

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

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

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
>

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

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

Bob

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

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

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
>

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.*

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

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
>>>
>>

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
>>
>

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
>

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

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

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.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

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/

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

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

Great. I will test with the next release


 Dr. Angel Herráez
 Biochemistry and Molecular Biology,
 Dept. of Systems Biology, University of Alcalá
 E-28805 Alcalá de Henares  (Madrid), Spain
________________________________
De: Robert Hanson via Jmol-developers <jmo...@li...>
Enviado: miércoles, 7 de febrero de 2024 18:40
Para: jmo...@li... <jmo...@li...>
Cc: Robert Hanson <ha...@st...>
Asunto: Re: [Jmol-developers] localization missing in 16.1.53

ATENCIÓN: Este correo electrónico se envió desde fuera de la UAH. No haga clic en enlaces ni abra archivos adjuntos a menos que reconozca al remitente y sepa que el contenido es seguro.
Angel, the problem was that I got rid of that directory in favor of just leaving it where it resides in org/jmol/translation/JmolApplet, but forgot to then connect that up with the menu. That is corrected.
Bob

Angel, the problem was that I got rid of that directory in favor of just
leaving it where it resides in org/jmol/translation/JmolApplet, but forgot
to then connect that up with the menu. That is corrected.
Bob

OK, thanks, Angel.

Hi Bob

I just downloaded 16.1.53 zip distribution and I notice the absence of 
the "idioma" folder inside jsmol.zip


·
  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/

FEBS Education and Training Conference <https://FEBSETC.org>