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Re: [Jmol-users] Jmol-users Digest, Vol 235, Issue 12

[Greeves, N. <ngr...@li...>]

All this discussion of STL files reminds me of our efforts to 3D print transition states for selected organic reactions.

STL files were one of the three outputs supported. XYZ and X3D were the others. They are free to download obviously.

<https://www.chemtube3d.com/3dprintingpage/>
3D Printing of Selected Transition States<https://www.chemtube3d.com/3dprintingpage/>
chemtube3d.com<https://www.chemtube3d.com/3dprintingpage/>
[apple-touch-icon.png]<https://www.chemtube3d.com/3dprintingpage/>

All the best
Nick
Sent from my iPhone

On 8 Dec 2025, at 11:22, jmo...@li... wrote:

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Today's Topics:

  1. Re: STL File Question (Angel Herraez)


----------------------------------------------------------------------

Message: 1
Date: Mon, 8 Dec 2025 11:22:08 +0000
From: Angel Herraez <ang...@ua...>
To: "jmo...@li..."
   <jmo...@li...>
Subject: Re: [Jmol-users] STL File Question
Message-ID:
   <AM4...@AM...>

Content-Type: text/plain; charset="utf-8"

Another online viewer that can also be embedded in your own webpage (Jaime Prilusky has done this trick of embedding for our 3Dprint project being developed inside Proteopedia)


Dr. Angel Herr?ez
Biochemistry and Molecular Biology,
Dept. of Systems Biology, University of Alcal?
E-28805 Alcal? de Henares  (Madrid), Spain
________________________________
De: Mark Perri <pe...@so...>
Enviado: lunes, 8 de diciembre de 2025 6:17
Para: jmo...@li... <jmo...@li...>
Asunto: Re: [Jmol-users] STL File Question

ATENCI?N: Este correo electr?nico se envi? 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.
They can also be loaded in online viewers (I found viewstl.com<http://viewstl.com/> for example).   This was my favorite one to 3d-print.

[image.png]

On Sun, Dec 7, 2025 at 8:41?PM Otie Rothenberger <oti...@gm...<mailto:oti...@gm...>> wrote:
One more observation. I can drag the grey ipad files to the apps display box, and the load perfectly!
--
Otis Rothenberger
oti...@gm...<mailto:oti...@gm...>
https://chemagic.org<https://chemagic.org/>

On Dec 7, 2025, at 11:49?AM, Robert Hanson via Jmol-users <jmo...@li...<mailto:jmo...@li...>> wrote:

?
Otis, have you tried loading them at an online service such as https://www.viewstl.com<https://www.viewstl.com/> ?

load =ams/quartz 1 packed
select @13
polyhedra UNITCELL
write t.stl

displayed for me properly as
<image.png>

Bob

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End of Jmol-users Digest, Vol 235, Issue 12
*******************************************

Re: [Jmol-users] STL File Question

[Jaime P. <jai...@we...>]

The online viewer is at https://3dviewer.net/

The source of the STL/OBJviewer is at https://github.com/kovacsv/Online3DViewer

Please let me know if you need help integrating it to your site.

Jaim

On 8 Dec 2025, at 13:22, Angel Herraez <ang...@ua...> wrote:

Another online viewer that can also be embedded in your own webpage (Jaime Prilusky has done this trick of embedding for our 3Dprint project being developed inside Proteopedia)


 Dr. Angel Herráez
 Biochemistry and Molecular Biology,
 Dept. of Systems Biology, University of Alcalá
 E-28805 Alcalá de Henares  (Madrid), Spain
________________________________
De: Mark Perri <pe...@so...<mailto:pe...@so...>>
Enviado: lunes, 8 de diciembre de 2025 6:17
Para: jmo...@li...<mailto:jmo...@li...> <jmo...@li...<mailto:jmo...@li...>>
Asunto: Re: [Jmol-users] STL File Question

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.
They can also be loaded in online viewers (I found viewstl.com<http://viewstl.com/> for example).   This was my favorite one to 3d-print.

<image.png>

On Sun, Dec 7, 2025 at 8:41 PM Otie Rothenberger <oti...@gm...<mailto:oti...@gm...>> wrote:
One more observation. I can drag the grey ipad files to the apps display box, and the load perfectly!
--
Otis Rothenberger
oti...@gm...<mailto:oti...@gm...>
https://chemagic.org<https://chemagic.org/>

On Dec 7, 2025, at 11:49 AM, Robert Hanson via Jmol-users <jmo...@li...<mailto:jmo...@li...>> wrote:


Otis, have you tried loading them at an online service such as https://www.viewstl.com<https://www.viewstl.com/> ?

load =ams/quartz 1 packed
select @13
polyhedra UNITCELL
write t.stl

displayed for me properly as
<image.png>

Bob

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Re: [Jmol-users] STL File Question

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

Another online viewer that can also be embedded in your own webpage (Jaime Prilusky has done this trick of embedding for our 3Dprint project being developed inside Proteopedia)


 Dr. Angel Herráez
 Biochemistry and Molecular Biology,
 Dept. of Systems Biology, University of Alcalá
 E-28805 Alcalá de Henares  (Madrid), Spain
________________________________
De: Mark Perri <pe...@so...>
Enviado: lunes, 8 de diciembre de 2025 6:17
Para: jmo...@li... <jmo...@li...>
Asunto: Re: [Jmol-users] STL File Question

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.
They can also be loaded in online viewers (I found viewstl.com<http://viewstl.com/> for example).   This was my favorite one to 3d-print.

[image.png]

On Sun, Dec 7, 2025 at 8:41 PM Otie Rothenberger <oti...@gm...<mailto:oti...@gm...>> wrote:
One more observation. I can drag the grey ipad files to the apps display box, and the load perfectly!
--
Otis Rothenberger
oti...@gm...<mailto:oti...@gm...>
https://chemagic.org<https://chemagic.org/>

On Dec 7, 2025, at 11:49 AM, Robert Hanson via Jmol-users <jmo...@li...<mailto:jmo...@li...>> wrote:


Otis, have you tried loading them at an online service such as https://www.viewstl.com<https://www.viewstl.com/> ?

load =ams/quartz 1 packed
select @13
polyhedra UNITCELL
write t.stl

displayed for me properly as
<image.png>

Bob

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Re: [Jmol-users] STL File Question

[Mark P. <pe...@so...>]

They can also be loaded in online viewers (I found viewstl.com for
example).   This was my favorite one to 3d-print.

[image: image.png]

On Sun, Dec 7, 2025 at 8:41 PM Otie Rothenberger <
oti...@gm...> wrote:

> One more observation. I can drag the grey ipad files to the apps display
> box, and the load perfectly!
> --
> Otis Rothenberger
> oti...@gm...
> https://chemagic.org
>
> On Dec 7, 2025, at 11:49 AM, Robert Hanson via Jmol-users <
> jmo...@li...> wrote:
>
> 
> Otis, have you tried loading them at an online service such as
> https://www.viewstl.com ?
>
> load =ams/quartz 1 packed
> select @13
> polyhedra UNITCELL
> write t.stl
>
> displayed for me properly as
> <image.png>
>
> Bob
>
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>

Re: [Jmol-users] radial plots

[Mark P. <pe...@so...>]

Hi Bob,

A user wanted to show their class the distance that radial nodes were at in
atoms larger than hydrogen.  I thought that calculating them and displaying
a radial distribution (probability?) function would be neat to look at.  I
saw your demo page and was wondering if it could be adapted to this for
atoms where the orbitals were calculated (e.g. GAMESS).

I can do this in python from a .cube file by reading the wavefunction for
an s-orbital along an axis.  But it would be neat if I could put it on the
js side of the code next to Jsmol displaying the orbital.  (e.g. 3s orbital
in Neon)

Thanks,
Mark

On Sun, Dec 7, 2025 at 1:01 AM Robert Hanson via Jmol-users <
jmo...@li...> wrote:

> No it doesn't. So you want to remove all angular components? Give me a
> hint what that is useful for. What exactly is the function you are looking
> for? Literature reference?
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>

Re: [Jmol-users] STL File Question

[Otie R. <oti...@gm...>]

<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto">One more observation. I can drag the grey ipad files to the apps display box, and the load perfectly!<br id="lineBreakAtBeginningOfSignature"><div dir="ltr"><div><span style="font-size: 28pt;">--</span></div><div><div>Otis Rothenberger</div><div>oti...@gm...</div><div>https://chemagic.org</div></div></div><div dir="ltr"><br><blockquote type="cite">On Dec 7, 2025, at 11:49 AM, Robert Hanson via Jmol-users &lt;jmo...@li...&gt; wrote:<br><br></blockquote></div><blockquote type="cite"><div dir="ltr"><div dir="ltr"><div>Otis, have you tried loading them at an online service such as&nbsp;<a href="https://www.viewstl.com">https://www.viewstl.com</a> ?</div><div><br></div><div>load =ams/quartz 1 packed</div><div>select&nbsp;@13</div><div>polyhedra UNITCELL</div><div>write t.stl</div><div><br></div><div>displayed for me properly as</div><div><div>&lt;image.png&gt;</div><br></div><div>Bob</div><div><br></div></div>
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Re: [Jmol-users] STL File Question

[Otie R. <oti...@gm...>]

<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto">Bob,<div><br></div><div>This display link is a VERY big help. The web display page is helping me communicate with the high school teachers who are actually working with printers. I know they are going to like this also.</div><div><br></div><div>It does not work on my iPad because on the iPad side the local STL files are greyed out - i.e not available for loading. I think I mentioned this previously. I don't fully understand that, but I'll work with my Mac when I'm working with the teachers.</div><div><br></div><div>I know that this group of teachers are really going to like this display page also. They are also about to fall in love with Jmol!</div><div><br id="lineBreakAtBeginningOfSignature"><div dir="ltr"><div><span style="font-size: 28pt;">--</span></div><div><div>Otis Rothenberger</div><div>oti...@gm...</div><div>https://chemagic.org</div></div></div><div dir="ltr"><br><blockquote type="cite">On Dec 7, 2025, at 11:49 AM, Robert Hanson via Jmol-users &lt;jmo...@li...&gt; wrote:<br><br></blockquote></div><blockquote type="cite"><div dir="ltr"><div dir="ltr"><div>Otis, have you tried loading them at an online service such as&nbsp;<a href="https://www.viewstl.com">https://www.viewstl.com</a> ?</div><div><br></div><div>load =ams/quartz 1 packed</div><div>select&nbsp;@13</div><div>polyhedra UNITCELL</div><div>write t.stl</div><div><br></div><div>displayed for me properly as</div><div><div>&lt;image.png&gt;</div><br></div><div>Bob</div><div><br></div></div>
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Re: [Jmol-users] STL File Question

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

let me know if you find any STL files made by Jmol that do not work in your
reader.

Re: [Jmol-users] STL File Question

[Otie R. <oti...@gm...>]

Thanks Bob,

Messing with versions was not a smart move on my part. I have to go back to my starting point and clear cache. I guess moving to the latest version and clearing cache would be a smart move!

I wan't paying much attention to this until high school teachers started talking to me about this. I did not realize that this (3d printers) had become a huge high school interest.

--
Otis Rothenberger
oti...@gm...
https://chemagic.org

> On Dec 7, 2025, at 4:40 PM, Robert Hanson via Jmol-users <jmo...@li...> wrote:
> 
> 
> There is unlikely anything relating to Jmol versions. There have been no significant changes since the STL writer was introduced in 2016.
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] STL File Question

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

There is unlikely anything relating to Jmol versions. There have been no
significant changes since the STL writer was introduced in 2016.

Re: [Jmol-users] STL File Question

[Otie R. <oti...@gm...>]

<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div dir="ltr"><meta http-equiv="content-type" content="text/html; charset=utf-8">Angel,<div><br></div><div>This is all very erratic. I actually was having success with Mac and no success with iPad. Now I am having problems with both. I need to work on this some more. I'll get back to the group with more specifics. I think the reason that I am having problems with my Mac today is that I changed my Mac JSmol version! &nbsp;<br id="lineBreakAtBeginningOfSignature"><div dir="ltr"><div><span style="font-size: 28pt;">--</span></div><div><div>Otis Rothenberger</div><div>oti...@gm...</div><div>https://chemagic.org</div></div></div><div dir="ltr"><br><blockquote type="cite">On Dec 7, 2025, at 2:14 PM, Angel Herraez &lt;ang...@ua...&gt; wrote:<br><br></blockquote></div><blockquote type="cite"><div dir="ltr">

<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">



<div class="elementToProof" style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Hello Otis</div>
<div class="elementToProof" style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
That's my first knowledge that Jmol/JSmol could read STL files. Can it?</div>
<div class="elementToProof" style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div class="elementToProof" id="Signature">
<div style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-size: 11pt;"><br>
&nbsp;Dr. Angel Herráez<br>
&nbsp;Biochemistry and Molecular Biology,<br>
&nbsp;Dept. of Systems Biology, University of Alcalá<br>
&nbsp;E-28805 Alcalá de Henares&nbsp; (Madrid), Spain</div>
</div>
<div id="appendonsend"></div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>De:</b> Otie Rothenberger &lt;oti...@gm...&gt;<br>
<b>Enviado:</b> domingo, 7 de diciembre de 2025 18:04<br>
<b>Para:</b> jmo...@li... &lt;jmo...@li...&gt;<br>
<b>Asunto:</b> [Jmol-users] STL File Question</font>
<div>&nbsp;</div>
</div>
<div dir="auto">
<div style="background-color:#E3F2FD; width:100%; padding:2pt; font-size:10pt; line-height:12pt; font-family:'Calibri'; color:black; border:1pt solid #9C6500">
<span style="color:#9c6500"><span style="color:#000000"><strong>ATENCIÓN</strong></span>:</span> 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.</div>
<div>STL saving and loading is working on my chemagic model kit via a Mac, but loading is not working on my iPad. I can save an STL file on my iPad, but I cannot load the file. The iPad will not even load an STL file that was created on my Mac. I'm not using
 the latest JSmol version on the chemagic site, but the ipad problem still exits if I use version&nbsp;<span style="font-family:UICTFontTextStyleBody">1603037 locally.</span>
<div><font face="UICTFontTextStyleBody"><span style=""><br>
</span></font></div>
<div><font face="UICTFontTextStyleBody"><span style="">I'm curious if any other Apple JSmol group members see an iPad problem with loading STL files that are created locally or elsewhere.</span></font></div>
<div><font face="UICTFontTextStyleBody"><span style=""><br>
</span></font></div>
<div>
<div class="" style="display:block">
<div class="x_apple-rich-link" role="link" data-url="https://chemagic.org/molecules/amini.html" style="display:inline-block">
<a class="x_lp-rich-link" rel="nofollow" href="https://chemagic.org/molecules/amini.html" originalsrc="https://chemagic.org/molecules/amini.html" dir="ltr" role="button" width="300" style="border-radius:10px; font-family:-apple-system,Helvetica,Arial,sans-serif; display:block; width:300px; overflow:hidden; text-decoration:none">
<table class="x_lp-rich-link-emailBaseTable" cellpadding="0" cellspacing="0" border="0" width="300" style="table-layout:fixed; border-collapse:collapse; width:300px; background-color:#E9E9EB; font-family:-apple-system,Helvetica,Arial,sans-serif">
<tbody>
<tr>
<td>
<table bgcolor="#E9E9EB" cellpadding="0" cellspacing="0" width="300" class="x_lp-rich-link-captionBar" style="font-family:-apple-system,Helvetica,Arial,sans-serif; table-layout:fixed; background-color:rgba(233,233,235,1)">
<tbody>
<tr>
<td class="x_lp-rich-link-captionBar-textStackItem" style="padding:8px 0px 8px 0px">
<div class="x_lp-rich-link-captionBar-textStack" style="max-width:100%; margin:0px 16px 0px 16px; overflow:hidden">
<div class="x_lp-rich-link-captionBar-textStack-topCaption-leading" style="word-wrap:break-word; font-weight:500; font-size:12px; overflow:hidden; text-overflow:ellipsis; text-align:left">
<a rel="nofollow" href="https://chemagic.org/molecules/amini.html" originalsrc="https://chemagic.org/molecules/amini.html" style="text-decoration:none"><font color="#000000" style="color:rgba(0,0,0,1)">Virtual Molecular Model Kit - Vmols</font></a></div>
<div class="x_lp-rich-link-captionBar-textStack-bottomCaption-leading" style="word-wrap:break-word; font-weight:400; font-size:11px; overflow:hidden; text-overflow:ellipsis; text-align:left">
<a rel="nofollow" href="https://chemagic.org/molecules/amini.html" originalsrc="https://chemagic.org/molecules/amini.html" style="text-decoration:none"><font color="#A2A2A9" style="color:rgba(60,60,67,0.6)">chemagic.org</font></a></div>
</div>
</td>
<td class="x_lp-rich-link-captionBar-rightIconItem" width="36" style="padding:6px 12px 6px 0px">
<a rel="nofollow" href="https://chemagic.org/molecules/amini.html" originalsrc="https://chemagic.org/molecules/amini.html"><div>&lt;apple-touch-icon.png&gt;</div></a></td>
</tr>
</tbody>
</table>
</td>
</tr>
</tbody>
</table>
</a></div>
</div>
<div><br>
</div>
<div>
<div dir="ltr">
<div><span style="font-size:28pt">--</span></div>
<div>
<div>Otis Rothenberger</div>
<div>oti...@gm...</div>
<div>https://chemagic.org</div>
</div>
</div>
</div>
</div>
</div>
</div>


<span>_______________________________________________</span><br><span>Jmol-users mailing list</span><br><span>Jmo...@li...</span><br><span>https://lists.sourceforge.net/lists/listinfo/jmol-users</span><br></div></blockquote></div></div></body></html>

Re: [Jmol-users] STL File Question

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

Hello Otis
That's my first knowledge that Jmol/JSmol could read STL files. Can it?



 Dr. Angel Herráez
 Biochemistry and Molecular Biology,
 Dept. of Systems Biology, University of Alcalá
 E-28805 Alcalá de Henares  (Madrid), Spain
________________________________
De: Otie Rothenberger <oti...@gm...>
Enviado: domingo, 7 de diciembre de 2025 18:04
Para: jmo...@li... <jmo...@li...>
Asunto: [Jmol-users] STL File Question

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.
STL saving and loading is working on my chemagic model kit via a Mac, but loading is not working on my iPad. I can save an STL file on my iPad, but I cannot load the file. The iPad will not even load an STL file that was created on my Mac. I'm not using the latest JSmol version on the chemagic site, but the ipad problem still exits if I use version 1603037 locally.

I'm curious if any other Apple JSmol group members see an iPad problem with loading STL files that are created locally or elsewhere.

<https://chemagic.org/molecules/amini.html>
Virtual Molecular Model Kit - Vmols<https://chemagic.org/molecules/amini.html>
chemagic.org<https://chemagic.org/molecules/amini.html>
[apple-touch-icon.png]<https://chemagic.org/molecules/amini.html>

--
Otis Rothenberger
oti...@gm...
https://chemagic.org

Re: [Jmol-users] STL File Question

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

Otis, my question is: are STL files produced by JSmol in the iPad readable outside the iPad?
I would guess that JSmol is doing it correctly, only the iPad has no way to display the files.


 Dr. Angel Herráez
 Biochemistry and Molecular Biology,
 Dept. of Systems Biology, University of Alcalá
 E-28805 Alcalá de Henares  (Madrid), Spain
________________________________
De: Otie Rothenberger <oti...@gm...>
Enviado: domingo, 7 de diciembre de 2025 20:10
Para: jmo...@li... <jmo...@li...>
Asunto: Re: [Jmol-users] STL File Question

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.
Bob,

With the problem clearly being a problem with the iPad operating system, does this AI suggestion have any JSmol possibility?

From AI:

Apps Provide Support: iPadOS itself doesn't natively open STL files like a photo, but powerful apps leverage the operating system to read and process them.
Import via Files App: You can download or save an STL file to your iPad's Files app, then use the "Import" feature within a 3D app to select and load it.
--
Otis Rothenberger
oti...@gm...
https://chemagic.org

On Dec 7, 2025, at 11:49 AM, Robert Hanson via Jmol-users <jmo...@li...> wrote:


Otis, have you tried loading them at an online service such as https://www.viewstl.com<https://www.viewstl.com/> ?

load =ams/quartz 1 packed
select @13
polyhedra UNITCELL
write t.stl

displayed for me properly as
<image.png>

Bob

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Jmol-users mailing list
Jmo...@li...
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] STL File Question

[Otie R. <oti...@gm...>]

<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto">Bob,<div><br></div><div>With the problem clearly being a problem with the iPad operating system, does this AI suggestion have any JSmol possibility?&nbsp;</div><div><br></div><div>From AI:</div><div><br></div><div><div>Apps Provide Support: iPadOS itself doesn't natively open STL files like a photo, but powerful apps leverage the operating system to read and process them.</div><div>Import via Files App: You can download or save an STL file to your iPad's Files app, then use the "<b>Import" feature</b> within a 3D app to select and load it.</div><div dir="ltr"><div><span style="font-size: 28pt;">--</span></div><div><div>Otis Rothenberger</div><div>oti...@gm...</div><div>https://chemagic.org</div></div></div><div dir="ltr"><br><blockquote type="cite">On Dec 7, 2025, at 11:49 AM, Robert Hanson via Jmol-users &lt;jmo...@li...&gt; wrote:<br><br></blockquote></div><blockquote type="cite"><div dir="ltr"><div dir="ltr"><div>Otis, have you tried loading them at an online service such as&nbsp;<a href="https://www.viewstl.com">https://www.viewstl.com</a> ?</div><div><br></div><div>load =ams/quartz 1 packed</div><div>select&nbsp;@13</div><div>polyhedra UNITCELL</div><div>write t.stl</div><div><br></div><div>displayed for me properly as</div><div><div>&lt;image.png&gt;</div><br></div><div>Bob</div><div><br></div></div>
<span>_______________________________________________</span><br><span>Jmol-users mailing list</span><br><span>Jmo...@li...</span><br><span>https://lists.sourceforge.net/lists/listinfo/jmol-users</span><br></div></blockquote></div></body></html>

Re: [Jmol-users] STL File Question

[Otie R. <oti...@gm...>]

<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto">Bob,<div><br></div><div>Thanks. Apple is really the problem here! When I follow your link and attempt to load an stl file from a folder on my iPad, all stl files are grayed out. This is clearly an iPad problem. When I did a further web search on this issue, it became clear that this is an iPad problem encountered by a really large number of people. I guess I'm lucky that it at least works on a Mac.</div><div><br></div><div>As you probably know, I do a lot of CheMagic/JSmol work in high school teaching groups, and stl work is really a hot item in this group right now. Of course, this is all connected with the 3D printers that this group is currently using in their classes.</div><div><br></div><div><br id="lineBreakAtBeginningOfSignature"><div dir="ltr"><div><span style="font-size: 28pt;">--</span></div><div><div>Otis Rothenberger</div><div>oti...@gm...</div><div>https://chemagic.org</div></div></div><div dir="ltr"><br><blockquote type="cite">On Dec 7, 2025, at 11:49 AM, Robert Hanson via Jmol-users &lt;jmo...@li...&gt; wrote:<br><br></blockquote></div><blockquote type="cite"><div dir="ltr"><div dir="ltr"><div>Otis, have you tried loading them at an online service such as&nbsp;<a href="https://www.viewstl.com">https://www.viewstl.com</a> ?</div><div><br></div><div>load =ams/quartz 1 packed</div><div>select&nbsp;@13</div><div>polyhedra UNITCELL</div><div>write t.stl</div><div><br></div><div>displayed for me properly as</div><div><div>&lt;image.png&gt;</div><br></div><div>Bob</div><div><br></div></div>
<span>_______________________________________________</span><br><span>Jmol-users mailing list</span><br><span>Jmo...@li...</span><br><span>https://lists.sourceforge.net/lists/listinfo/jmol-users</span><br></div></blockquote></div></body></html>

Re: [Jmol-users] STL File Question

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

So this would be a problem of the iPad not having some software that reads STL files. Windows does not have one usually by default.


 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-users <jmo...@li...>
Enviado: domingo, 7 de diciembre de 2025 18:48
Para: jmo...@li... <jmo...@li...>
Cc: Robert Hanson <ha...@st...>
Asunto: Re: [Jmol-users] STL File Question

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.
Otis, have you tried loading them at an online service such as https://www.viewstl.com<https://www.viewstl.com/> ?

load =ams/quartz 1 packed
select @13
polyhedra UNITCELL
write t.stl

displayed for me properly as
[image.png]
Bob

Re: [Jmol-users] STL File Question

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

Otis, have you tried loading them at an online service such as
https://www.viewstl.com ?

load =ams/quartz 1 packed
select @13
polyhedra UNITCELL
write t.stl

displayed for me properly as
[image: image.png]
Bob

[Jmol-users] STL File Question

[Otie R. <oti...@gm...>]

<html><head><meta http-equiv="content-type" content="text/html; charset=us-ascii"></head><body dir="auto">STL saving and loading is working on my chemagic model kit via a Mac, but loading is not working on my iPad. I can save an STL file on my iPad, but I cannot load the file. The iPad will not even load an STL file that was created on my Mac. I'm not using the latest JSmol version on the chemagic site, but the ipad problem still exits if I use version&nbsp;<span style="font-family: UICTFontTextStyleBody; -webkit-text-size-adjust: auto;">1603037 locally.</span><div><font face="UICTFontTextStyleBody"><span style="-webkit-text-size-adjust: auto;"><br></span></font></div><div><font face="UICTFontTextStyleBody"><span style="-webkit-text-size-adjust: auto;">I'm curious if any other Apple JSmol group members see an iPad problem with loading STL files that are created locally or elsewhere.</span></font></div><div><font face="UICTFontTextStyleBody"><span style="-webkit-text-size-adjust: auto;"><br></span></font></div><div><div style="display: block;" class=""><div style="-webkit-user-select: all; -webkit-user-drag: element; display: inline-block;" class="apple-rich-link" draggable="true" role="link" data-url="https://chemagic.org/molecules/amini.html"><a style="border-radius:10px;font-family:-apple-system, Helvetica, Arial, sans-serif;display:block;-webkit-user-select:none;width:300px;user-select:none;-webkit-user-modify:read-only;user-modify:read-only;overflow:hidden;text-decoration:none;" class="lp-rich-link" rel="nofollow" href="https://chemagic.org/molecules/amini.html" dir="ltr" role="button" draggable="false" width="300"><table style="table-layout:fixed;border-collapse:collapse;width:300px;background-color:#E9E9EB;font-family:-apple-system, Helvetica, Arial, sans-serif;" class="lp-rich-link-emailBaseTable" cellpadding="0" cellspacing="0" border="0" width="300"><tbody><tr><td vertical-align="center"><table bgcolor="#E9E9EB" cellpadding="0" cellspacing="0" width="300" style="font-family:-apple-system, Helvetica, Arial, sans-serif;table-layout:fixed;background-color:rgba(233, 233, 235, 1);" class="lp-rich-link-captionBar"><tbody><tr><td style="padding:8px 0px 8px 0px;" class="lp-rich-link-captionBar-textStackItem"><div style="max-width:100%;margin:0px 16px 0px 16px;overflow:hidden;" class="lp-rich-link-captionBar-textStack"><div style="word-wrap:break-word;font-weight:500;font-size:12px;overflow:hidden;text-overflow:ellipsis;text-align:left;" class="lp-rich-link-captionBar-textStack-topCaption-leading"><a rel="nofollow" href="https://chemagic.org/molecules/amini.html" style="text-decoration: none" draggable="false"><font color="#000000" style="color: rgba(0, 0, 0, 1);">Virtual Molecular Model Kit - Vmols</font></a></div><div style="word-wrap:break-word;font-weight:400;font-size:11px;overflow:hidden;text-overflow:ellipsis;text-align:left;" class="lp-rich-link-captionBar-textStack-bottomCaption-leading"><a rel="nofollow" href="https://chemagic.org/molecules/amini.html" style="text-decoration: none" draggable="false"><font color="#A2A2A9" style="color: rgba(60, 60, 67, 0.6);">chemagic.org</font></a></div></div></td><td style="padding:6px 12px 6px 0px;" class="lp-rich-link-captionBar-rightIconItem" width="36"><a rel="nofollow" href="https://chemagic.org/molecules/amini.html" draggable="false"><img style="pointer-events:none !important;display:inline-block;width:36px;height:36px;border-radius:3px;" width="36" height="36" draggable="false" class="lp-rich-link-captionBar-rightIcon" alt="apple-touch-icon.png" src="cid:0ACBC7FE-7454-481D-839C-C0A5128DF201"></a></td></tr></tbody></table></td></tr></tbody></table></a></div></div><div><br></div><div><div dir="ltr"><div><span style="font-size: 28pt;">--</span></div><div><div>Otis Rothenberger</div><div>oti...@gm...</div><div>https://chemagic.org</div></div></div></div></div></body></html>

Re: [Jmol-users] radial plots

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

No it doesn't. So you want to remove all angular components? Give me a hint
what that is useful for. What exactly is the function you are looking for?
Literature reference?

[Jmol-users] radial plots

[Mark P. <pe...@so...>]

Hi Everyone,

Does Jmol calculate radial distribution functions for electrons from MO
outputs from computational packages?  I found this:
https://chemapps.stolaf.edu/jmol/orbitals/ but it looks like these are just
hydrogen-like orbitals. Can something similar be done with MOs from an
output file?

Thanks,
Mark

Re: [Jmol-users] Jmol in Crystallography

[Mark P. <pe...@so...>]

Open up dev tools, go to network, disable cache, and reload your page.

On Wed, Dec 3, 2025 at 3:12 PM Carroll, Patrick J <car...@sa...>
wrote:

> Bob,
>
>         How do you do that speed measurement? Is that something I can do
> so I can show it to the IT guys?
>
> Pat
>
>
> Sent from my iPhone while enjoying a very dry martini
>
> > On Dec 3, 2025, at 2:25 PM, Robert Hanson via Jmol-users <
> jmo...@li...> wrote:
> >
> > 
> > No, actually it is just extremely slow. Or was. 800 ms for 25 kb??
> > _______________________________________________
> > Jmol-users mailing list
> > Jmo...@li...
> >
> https://urldefense.com/v3/__https://lists.sourceforge.net/lists/listinfo/jmol-users__;!!IBzWLUs!Rs41Y0cKDdq5Ji9ao36T9xZgRC5xj4DS95BD7Nb3Kjv3udTC0BxSLS-NPWjKunGqdU5s2JTNqA0Q5MMKXTo67BgkhoA4Fr0U$
>
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>

Re: [Jmol-users] Jmol in Crystallography

[Carroll, P. J <car...@sa...>]

Bob,

        How do you do that speed measurement? Is that something I can do so I can show it to the IT guys?

Pat


Sent from my iPhone while enjoying a very dry martini

> On Dec 3, 2025, at 2:25 PM, Robert Hanson via Jmol-users <jmo...@li...> wrote:
> 
> 
> No, actually it is just extremely slow. Or was. 800 ms for 25 kb??
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://urldefense.com/v3/__https://lists.sourceforge.net/lists/listinfo/jmol-users__;!!IBzWLUs!Rs41Y0cKDdq5Ji9ao36T9xZgRC5xj4DS95BD7Nb3Kjv3udTC0BxSLS-NPWjKunGqdU5s2JTNqA0Q5MMKXTo67BgkhoA4Fr0U$

Re: [Jmol-users] Jmol in Crystallography

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

No, actually it is just extremely slow. Or was. 800 ms for 25 kb??

Re: [Jmol-users] Jmol in Crystallography

[Carroll, P. J <car...@sa...>]

Bob,

       In your earlier e-mail, you remarked that my server was slow. I assume that is because I always load a full cell (and sometimes more, for packing diagrams). Even for displaying single molecules, I use load "" centroid; display within (molecule, !symmetry) so I can "grow" the molecule if it lies on a symmetry element (e.g., 1274.html). For packing diagrams, I use load {444 666 0} routinely (e.,g., 1462c.html) or even load {333 777 0} (in 1144cell.html). You should see when I try to load a cubic cell with 96 molecules - I can go get a cup of coffee and watch an episode of "Keeping Up with the Kardashians"!


Pat




________________________________________
From: Robert Hanson via Jmol-users <jmo...@li...>
Sent: Monday, December 1, 2025 11:04 PM
To: jmo...@li...
Cc: Robert Hanson
Subject: Re: [Jmol-users] Jmol in Crystallography

Nice to hear from you, Pat! Ah, yes....PARTS...

[image.png][image.png]

That was a nice addition. Thank you for pointing out the need for that and helping me get it right.

I wonder why your server is so slow:

[image.png]

Maybe because it is http and not https?

Are these buttons supposed to do something?

[image.png]

Wait, now I see it. I have to press "add" -- NICE!

[image.png]



Have you played with the new MODELKIT command? See

https://journals.iucr.org/j/issues/2024/05/00/dv5017/index.html<https://urldefense.com/v3/__https://journals.iucr.org/j/issues/2024/05/00/dv5017/index.html__;!!IBzWLUs!UUgM-_Z6YgqDrkjVuHV0DGUT7a1p9fMAf8SDNmHZpc0fPR5NIRufVqSfQAtu-vZ0YinZ_bxecwI6bHl6ONtyamcdtfH9e_eO$>

and

https://chemapps.stolaf.edu/jmol/jsmol/iucrdemo/<https://urldefense.com/v3/__https://chemapps.stolaf.edu/jmol/jsmol/iucrdemo/__;!!IBzWLUs!UUgM-_Z6YgqDrkjVuHV0DGUT7a1p9fMAf8SDNmHZpc0fPR5NIRufVqSfQAtu-vZ0YinZ_bxecwI6bHl6ONtyamcdtSg7yxFH$>

Wow, this goes on and on!!!

Fantastic. Is there an index?

Going to Calgary? https://www.iucr2026.org/<https://urldefense.com/v3/__https://www.iucr2026.org/__;!!IBzWLUs!UUgM-_Z6YgqDrkjVuHV0DGUT7a1p9fMAf8SDNmHZpc0fPR5NIRufVqSfQAtu-vZ0YinZ_bxecwI6bHl6ONtyamcdtT80kFxw$>
I'm hoping to make a couple of presentations there.

Bob

Re: [Jmol-users] Using Jmol in Crystallography

[Giuseppe S. <giu...@gm...>]

Hi all, that's right in this form
http://macxray.chem.upenn.edu/aca09/index.html it works.
Thanks and best regards
Giuseppe

Il giorno mar 2 dic 2025 alle ore 15:47 Robert Hanson via Jmol-users <
jmo...@li...> ha scritto:

> Pat,
>
> Looks like you need to indicate the file name explicitly. Not just the
> directory. That's a server side setting. For some reason it is not enabled
> at Penn.
>
> http://macxray.chem.upenn.edu/aca09/index.html
>
> And better is https in terms of suggestions for people
>
> https://macxray.chem.upenn.edu/aca09/index.html
>
> But not this
>
> https://macxray.chem.upenn.edu/aca09
>
> I would love to see you present a summary of your innovative
> implementations at another ACA or IUCr meeting, Pat. You helped a lot along
> the way to get many of these features into Jmol.
>
> I plan to give a couple of talks in Calgary.
>
>  There's at least one education symposium and probably more. Jmol will be
> featured in a plenary on a new mathematical way to describe magnetic
> structures involving some new visualizations of magnetic point groups we
> are developing.
>
> https://findspingroup.com
>
> That was the subject of my visit to Shenzhen China last week. Space group
> on the left. Spin point group on the right.
>
>
>
>
>
> This uses a new feature I added that allows displaying two frames side by
> side in a split panel mode. Should be generally useful. Not yet released.
>
> Bob
>
>
>>
>>
>>
>> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>