jmol-users Mailing List for Jmol

 Jmol-16.3.37-binary.zip (82.1 MB)
<https://sourceforge.net/projects/jmol/files/latest/download>
*Important Note*: Any page accessing the American Mineralogist Society
Crystal Structure Database using the "load =ams/" shortcut requires this
update, as their API call and domain have been changed.
Other updates in this release include an upgrade to JavaScript 2D JSME
version 2024年04月29日, a fix for MOLDEN file reading for molecular orbitals
where G orbitals are present (though still ignored), and a fix that removes
the overloading of the JavaScript String.concat() method, which was not
actually needed for JSmol anyway.
*Jmol.___JmolVersion="16.3.37" // (legacy) also 16.3.38 (swingJS) *
feature change: American Mineralogist Society Crystal Structure Database
new target API
 -- load =ams/quartz
 -- was
https://rruff.geo.arizona.edu/AMS/viewJmol.php?mineral=quartz&action=showcif
 -- now
https://www.rruff.net/AMS/jsmol_search.php?mineral=quartz&filetype=cif
 -- effective 2025年11月16日
bug fix: MO calculation fails when G orbitals are present
 -- broken in 16.1.45
bug fix (legacy JavaScript only): JavaScript String.concat()
 -- does not allow for multiple parameters
 -- does not need to check for null, since Jmol will never do that
 -- overwritten method removed in JmolJavaExt.js
 -- see appletweb/jsmol.js for prerelease update
feature change (legacy JavaScript only): update to JSME_2024年04月29日
 -- see ref/JSME_2024年04月29日.zip
 -- site/swingjs/js/JSmolJME.js adjusted accordingly
 -- see appletweb/jsmol.js for prerelease update
Thank you to all who have identified these issues.
Bob Hanson

Hi John
frame pause
frame play
frame prev
frame next
https://chemapps.stolaf.edu/jmol/docs/#frame

Thanks Bob!
Also, I missed the right-click popup menu which has "pause' "resume" and
"stop" options under animation..
John K.
On Tue, Nov 11, 2025 at 2:15 PM Robert Hanson via Jmol-users <
jmo...@li...> wrote:
> see
> https://chemapps.stolaf.edu/jmol/docs/index.htm?command=animation&ver=16.3
>
> animation ON/OFF{default: ON}
>
> *Turns on or off animation. With animation ON, the frame
> <https://chemapps.stolaf.edu/jmol/docs/index.htm?ver=16.3#frame> range is
> also reset to all frames. (An implicit frame range ALL command is executed.
> This functionality is for backward compatibility with Chime.) If this
> resetting is not desired because the frame range has been set, then frame
> PLAY or frame PLAYREV should be used instead of animation ON.*
>
>
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>

see
https://chemapps.stolaf.edu/jmol/docs/index.htm?command=animation&ver=16.3
animation ON/OFF{default: ON}
*Turns on or off animation. With animation ON, the frame
<https://chemapps.stolaf.edu/jmol/docs/index.htm?ver=16.3#frame> range is
also reset to all frames. (An implicit frame range ALL command is executed.
This functionality is for backward compatibility with Chime.) If this
resetting is not desired because the frame range has been set, then frame
PLAY or frame PLAYREV should be used instead of animation ON.*

Dear All,
OK, "anim off" stops a Jmol animation (v 16.1.45). But the next "anim on"
command restarts at frame 1. How do I stop/restart at the same frame?
Also, it would be useful if the above stop/restart functions could be
assigned to the toolbar arrow icons, or to other toolbar icons. I know that
holding down the forward or reverse arrow icons there runs the animation in
those directions. The problem is, when I do that, the mouse is not free to
navigate the molecular display (rotate/zoom etc).
John Keller

This fix is checked in as jsmol.zip as a prerelease of Jmol 16.32.37 in
https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/appletweb/. That
code block has been removed.
There was never a need for the overwriting of String.concat in the first
place, since Jmol will never send a null parameter to this method. (FYI,
Jmol/SwingJS avoids this problem entirely by using fully elaborated method
signatures for Java -- in this case String.prototype.concat$S)
Jmol.___JmolVersion="16.3.37" // (legacy) also 16.3.38 (swingJS)
bug fix (legacy JavaScript only): JavaScript String.concat()
 -- does not allow for multiple parameters
 -- does not need to check for null, since Jmol will never do that
 -- overwritten method removed in JmolJavaExt.js
 -- see appletweb/jsmol.js for prerelease update
feature change (legacy JavaScript only): update to JSME_2024年04月29日
 -- see ref/JSME_2024年04月29日.zip
 -- site/swingjs/js/JSmolJME.js adjusted accordingly
 -- see appletweb/jsmol.js for prerelease update
Bob
Robert M. Hanson
Professor of Chemistry, Emeritus
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
*We stand on the homelands of the Wahpekute Band of the Dakota Nation. We
honor with gratitude the people who have stewarded the land throughout the
generations and their ongoing contributions to this region. We acknowledge
the ongoing injustices that we have committed against the Dakota Nation,
and we wish to interrupt this legacy, beginning with acts of healing and
honest storytelling about this place.*
On Sun, Nov 9, 2025, 12:23 AM Mark Perri <pe...@so...> wrote:
> Hi Bob,
>
> It looks like jsmol is overwriting String.prototype.concat. In
> javascript it is supposed to take multiple arguments, but after I load
> jsmol (16.3.35), it ignores all but the first argument. I think it's
> overwriting javascript concat globally with a java version.
>
> d.$concat = d.concat;
> d.concat = function(a) {
> if (null == a)
> throw new NullPointerException;
> return this.$concat(a)
> }
>
> Thanks,
> Mark
>
>
>

OK, this is checked in as jsmol.zip in
https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/appletweb/ if you
want to test it, Angel.
Bob

Fantastic.
The issue you see with the arrow is that if you have an atom selected, JSME
reports a SMILES with a marker [..:1] for the selected atoms. This is
(perhaps no longer) accepted by NCI/CADD.
I have fixed that, but I see another issue that has to do with the "Enable
Editing" option.
On Sun, Nov 9, 2025 at 11:17 AM Angel Herraez <ang...@ua...> wrote:
> Hi Bob
> I retrieved Jmol-16.3.35-binary.zip and JSME_2024年04月29日.zip and run tests
> form local disk. All these are working as far as I can see:
>
> jsme.htm
> jsmetest.htm
> jsmetest2.htm
> jsmetest3.htm
> jsv.htm
> jsv_jme.htm
>
> In the last one, enabling the edit checkbox and using the atom selection
> (red halo), clicking on the arrow towards JSV brings an error about access
> to NCI server, but it does the same in
> https://chemapps.stolaf.edu/jmol/jsmol/jsv_jme.htm
> So I assume it is a temporary issue with NCI
>
>
> 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:* viernes, 7 de noviembre de 2025 18:31
> *Para:* jmo...@li... <jmo...@li...
> >
> *Cc:* Robert Hanson <ha...@st...>
> *Asunto:* Re: [Jmol-users] Jmol 16.3.35/16.3.36
>
> *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.
> Thanks for that reminder. Every once in a while I have considered that and
> worried that my hacks in that code won't be reproducible. But you are
> right. We should do that. Can you help me with that? Take a local jsmol
> unzipped directory and do the replacement, and see if the various JSME test
> pages still work. The one I am thinking of is the page jsv_jme.htm with the
> "enable editing" and blue selection dot.
>
> [image: image.png]
>
>
>
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
-- 
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.*

Hi Bob
I retrieved Jmol-16.3.35-binary.zip and JSME_2024年04月29日.zip and run tests form local disk. All these are working as far as I can see:
jsme.htm   
jsmetest.htm  
jsmetest2.htm 
jsmetest3.htm 
jsv.htm    
jsv_jme.htm  
In the last one, enabling the edit checkbox and using the atom selection (red halo), clicking on the arrow towards JSV brings an error about access to NCI server, but it does the same in https://chemapps.stolaf.edu/jmol/jsmol/jsv_jme.htm
So I assume it is a temporary issue with NCI
 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: viernes, 7 de noviembre de 2025 18:31
Para: jmo...@li... <jmo...@li...>
Cc: Robert Hanson <ha...@st...>
Asunto: Re: [Jmol-users] Jmol 16.3.35/16.3.36
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.
Thanks for that reminder. Every once in a while I have considered that and worried that my hacks in that code won't be reproducible. But you are right. We should do that. Can you help me with that? Take a local jsmol unzipped directory and do the replacement, and see if the various JSME test pages still work. The one I am thinking of is the page jsv_jme.htm with the "enable editing" and blue selection dot.
[image.png]

Hi Bob,
It looks like jsmol is overwriting String.prototype.concat. In
javascript it is supposed to take multiple arguments, but after I load
jsmol (16.3.35), it ignores all but the first argument. I think it's
overwriting javascript concat globally with a java version.
 d.$concat = d.concat;
 d.concat = function(a) {
 if (null == a)
 throw new NullPointerException;
 return this.$concat(a)
 }
Thanks,
Mark

OK, Bob
Right, I've been using just the basic draw functionalty in JSME (and transfer to a separate JSmol panel, back and forth) and not those other features.
I will test.
 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: viernes, 7 de noviembre de 2025 18:31
Para: jmo...@li... <jmo...@li...>
Cc: Robert Hanson <ha...@st...>
Asunto: Re: [Jmol-users] Jmol 16.3.35/16.3.36
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.
Thanks for that reminder. Every once in a while I have considered that and worried that my hacks in that code won't be reproducible. But you are right. We should do that. Can you help me with that? Take a local jsmol unzipped directory and do the replacement, and see if the various JSME test pages still work. The one I am thinking of is the page jsv_jme.htm with the "enable editing" and blue selection dot.
[image.png]
If that works, or there is a way to make that functionality work, I'm all for it.
But now I see that in build-1-just-unzip-to-site I have what was probably that commented out:
 <!--
 <echo>......adding jsme event hooks</echo>
 <replace dir="${site.jsmol.path}/jsme/jsme" includes="*.html" token="var c=arguments,d;" value="var c=arguments,d;if(!(d=(!c||!c[0]||!$wnd.Jmol?a:$wnd.Jmol._jmeHook(a, c[0]))))return;"/>
 -->
and I have commented all this out in JSmolJME.js:
// Jmol._jmeHook = function(a, e) {
// alert("hooked")
// // called from within function C(a) in JSME code
// // a is the function to send this event to using apply
// var d;
// return (!(d = e.target) || !(d._applet || (d = Jmol.$closest(d, 'div')[0])) || !d || !d._applet ? a : d._applet.__allowEvent(a, e));
// }
// proto.__allowEvent = function(a, e){
// alert("allowing event")
// var t;
// if(!e || !(t = e.target) || "DIV rect line text polygon ellipse path".indexOf("" + t.tagName) < 0){
// // cancel only these specific tags
// return a;
// }
//
// var isKey = (e.type.indexOf("key") >= 0);
// if (!this._editEnabled && isKey) {
/// // cancel all keyboard events
// return 0;
// }
// if ("dblclick mousedown mouseup".indexOf(e.type) < 0) {
// // cancel only these specific events
// return a;
// }
// var x = 200;
// var y = 200;
// try {
// x = parseInt(t.getAttribute("x"));//(t.textContent ? t.x.baseVal[0].value : t.points ? t.animatedPoints[0].x : isKey || !t.x && !t.x1 ? 200 : (t.x || t.x1).baseVal.value);
// y = parseInt(t.getAttribute("y"));//(t.textContent ? t.y.baseVal[0].value : t.points ? t.animatedPoints[0].y : isKey || !t.x && !t.x1 ? 200 : (t.y || t.y1).baseVal.value);
// } catch(e) {
// }
// // when editing is disabled, only the star key and main-panel clicking will be allowed
// var isStar = (x >= 100 && x < 124 && y < 24); // fifth icon from the left on top row
// var isMain = (x > 25 && y > 50 || x == 0 && y == 0 && t.width.baseVal.value > 100 && t.height.baseVal.value > 100);
// if (isStar || this._editEnabled && !isMain)
// this._starPressed = isStar;
// var ok = (isStar || this._editEnabled || isMain && this._starPressed);
// return (ok ? a : 0);
// }
I am thinking that what I am remembering is some very early efforts to hack that code, and I already have updated JME code in there that does this correctly.
So it will probably work just fine when you try that.
Bob
On Fri, Nov 7, 2025 at 7:03 AM Angel Herráez <ang...@ua...<mailto:ang...@ua...>> wrote:
Bob, maybe you can now find time to update the version of JSME included in the distribution? (10 years old)
In my pages I have been replacing it with newer versions without any troubles.
·
El 05/11/2025 a las 18:13, Robert Hanson via Jmol-users escribió:
Quite a variety of mostly specialized bugs here. A few changes for JSpecView in association with the IUPAC FAIRSpec project metadata extractor implementation.
Thank you to all who have contributed bug reports. GO, OPEN SOURCE!
Bob
Jmol.___JmolVersion="16.3.35" // (legacy) also 16.3.36 (swingJS)
bug fix (legacy only): JME interface not accepting MOL files with a blank first line
_______________________________________________
Jmol-users mailing list
Jmo...@li...<mailto:Jmo...@li...>
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
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.

Thanks for that reminder. Every once in a while I have considered that and
worried that my hacks in that code won't be reproducible. But you are
right. We should do that. Can you help me with that? Take a local jsmol
unzipped directory and do the replacement, and see if the various JSME test
pages still work. The one I am thinking of is the page jsv_jme.htm with the
"enable editing" and blue selection dot.
[image: image.png]
If that works, or there is a way to make that functionality work, I'm all
for it.
But now I see that in build-1-just-unzip-to-site I have what was probably
that commented out:
 <!--
 <echo>......adding jsme event hooks</echo>
 <replace dir="${site.jsmol.path}/jsme/jsme" includes="*.html"
token="var c=arguments,d;" value="var
c=arguments,d;if(!(d=(!c||!c[0]||!$wnd.Jmol?a:$wnd.Jmol._jmeHook(a,
c[0]))))return;"/>
 -->
and I have commented all this out in JSmolJME.js:
// Jmol._jmeHook = function(a, e) {
// alert("hooked")
// // called from within function C(a) in JSME code
// // a is the function to send this event to using apply
// var d;
// return (!(d = e.target) || !(d._applet || (d = Jmol.$closest(d,
'div')[0])) || !d || !d._applet ? a : d._applet.__allowEvent(a, e));
// }
// proto.__allowEvent = function(a, e){
// alert("allowing event")
// var t;
// if(!e || !(t = e.target) || "DIV rect line text polygon ellipse
path".indexOf("" + t.tagName) < 0){
// // cancel only these specific tags
// return a;
// }
//
// var isKey = (e.type.indexOf("key") >= 0);
// if (!this._editEnabled && isKey) {
/// // cancel all keyboard events
// return 0;
// }
// if ("dblclick mousedown mouseup".indexOf(e.type) < 0) {
// // cancel only these specific events
// return a;
// }
// var x = 200;
// var y = 200;
// try {
// x = parseInt(t.getAttribute("x"));//(t.textContent ?
t.x.baseVal[0].value : t.points ? t.animatedPoints[0].x : isKey || !t.x &&
!t.x1 ? 200 : (t.x || t.x1).baseVal.value);
// y = parseInt(t.getAttribute("y"));//(t.textContent ?
t.y.baseVal[0].value : t.points ? t.animatedPoints[0].y : isKey || !t.x &&
!t.x1 ? 200 : (t.y || t.y1).baseVal.value);
// } catch(e) {
// }
// // when editing is disabled, only the star key and main-panel clicking
will be allowed
// var isStar = (x >= 100 && x < 124 && y < 24); // fifth icon from the
left on top row
// var isMain = (x > 25 && y > 50 || x == 0 && y == 0 &&
t.width.baseVal.value > 100 && t.height.baseVal.value > 100);
// if (isStar || this._editEnabled && !isMain)
// this._starPressed = isStar;
// var ok = (isStar || this._editEnabled || isMain && this._starPressed);
// return (ok ? a : 0);
// }
I am thinking that what I am remembering is some very early efforts to hack
that code, and I already have updated JME code in there that does this
correctly.
So it will probably work just fine when you try that.
Bob
On Fri, Nov 7, 2025 at 7:03 AM Angel Herráez <ang...@ua...> wrote:
> Bob, maybe you can now find time to update the version of JSME included in
> the distribution? (10 years old)
>
> In my pages I have been replacing it with newer versions without any
> troubles.
>
> ·
>
> El 05/11/2025 a las 18:13, Robert Hanson via Jmol-users escribió:
>
> Quite a variety of mostly specialized bugs here. A few changes for
> JSpecView in association with the IUPAC FAIRSpec project metadata extractor
> implementation.
>
> Thank you to all who have contributed bug reports. GO, OPEN SOURCE!
>
> Bob
>
> Jmol.___JmolVersion="16.3.35" // (legacy) also 16.3.36 (swingJS)
>
> bug fix (legacy only): JME interface not accepting MOL files with a blank
> first line
>
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
-- 
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.*

Bob, maybe you can now find time to update the version of JSME included 
in the distribution? (10 years old)
In my pages I have been replacing it with newer versions without any 
troubles.
·
El 05/11/2025 a las 18:13, Robert Hanson via Jmol-users escribió:
> Quite a variety of mostly specialized bugs here. A few changes for 
> JSpecView in association with the IUPAC FAIRSpec project metadata 
> extractor implementation.
>
> Thank you to all who have contributed bug reports. GO, OPEN SOURCE!
>
> Bob
>
> Jmol.___JmolVersion="16.3.35" // (legacy) also 16.3.36 (swingJS)
>
> bug fix (legacy only): JME interface not accepting MOL files with a 
> blank first line

see
https://sourceforge.net/projects/jmol/files/Jmol/Version%2016.3/Jmol%2016335
Quite a variety of mostly specialized bugs here. A few changes for
JSpecView in association with the IUPAC FAIRSpec project metadata extractor
implementation.
Thank you to all who have contributed bug reports. GO, OPEN SOURCE!
Bob
Jmol.___JmolVersion="16.3.35" // (legacy) also 16.3.36 (swingJS)
feature change: Switching to new nmrdb prediction API for 1H and 13C
predicted spectra
 -- uses a POST of JSON
 -- see https://nmr-prediction.service.zakodium.com/v1/documentation/
 -- see https://chemapps.stolaf.edu/jmol/jsmol/testEPFL2.htm
 -- see https://chemapps.stolaf.edu/jmol/jsmol/testEPFL2-13C.htm
 -- see https://chemapps.stolaf.edu/jmol/jsmol/jsv_predict2.htm
new feature: COLOR ISOSURFACE VERTICES ({...}) green
 -- bit set of vertices to color
 -- generally not advised, but part of PyMOL session loading
bug fix: PyMOL surface translucency not read
 -- adds support for partially translucent PyMOL surfaces
bug fix: WRITE ISOSURFACE or WRITE xxx.jdxl creating unnecessarily large
files
 -- specifically for PyMOL files, size drops by up to 90% (500K to 50K)
bug fix: WRITE MESH not working
 -- should create a "vertex-only" (not linear marching cube) JVXL file
 -- these are much larger than the linear marching cube JVXL files
bug fix: coloring a read JVXL-based isosurface does not re-save new color
in write JVXL
bug fix: PDB files will not display unit cell with standard load
 -- broken in 16.2.24
bug fix: MOPAC v.23 not loading
 -- modified header not recognized
bug fix (legacy only): JME interface not accepting MOL files with a blank
first line
bug fix (legacy only): JSpecView interface fails for empty <peakInfo>
element
bug fix: various JSpecView upgrades
 -- expanded nmrML reading
 -- better JDX header processing for IUPAC FAIRSpec
 -- better connection between Jmol and JSpecView for reading
 files with both structure and spectra (JDX, nmrML)
bug fix: protein structure starting at residue 1 but not first in listing
not created
bug fix: SMILES generator for allenes broken in 16.3.10
-- 
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.*

If you have separate frames, which I think you do, just make sure you use
select 1.1
write "1.1.mol"
or something similar to that to select only the one frame.
If you have the frame as the current frame, you can use:
select this
or (as long as all the atoms are visible)
select visible
Bob
On Thu, Oct 16, 2025 at 12:37 PM John Keller via Jmol-users <
jmo...@li...> wrote:
> I have a large trajectory file as .xyz and I need to save one frame as a
> .mol file. I swear I have done this before, but now when I try this, either
> nothing is selected, or the whole trajectory is saved. Any suggestions?
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
-- 
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.*

I have a large trajectory file as .xyz and I need to save one frame as a
.mol file. I swear I have done this before, but now when I try this, either
nothing is selected, or the whole trajectory is saved. Any suggestions?

Hi John
your suggested
$delect hydrogen,carbon,oxygen,nitrogen
$ font label 15
did the job, saving me a lot of time
Thanks
Francesco
On Fri, Oct 10, 2025, 11:00 John Keller via Jmol-users <
jmo...@li...> wrote:
> Just zooming the molecule changes the relative size of the labels.
> Try this:
> load $glycerol;
> background white; color bonds gainsboro;
> select carbon,oxygen;
> label "%[atomno]"; set labelalignment center;
> font label 20 bold; color label yellow;
> ---------
> Then zoom it with mouse wheel.
>
> JOhn K.
>
>
> On Thu, Oct 9, 2025 at 11:48 PM Francesco Pietra <chi...@gm...>
> wrote:
>
>> Hello
>> Is any command to change the size of labels for all atoms at once?
>>
>> I have such a request by a referee about a submitted paper, as he wants
>> to see the molecule better. Displacing the labels is not enough
>>
>> Thanks
>>
>> Francesco Pietra
>> _______________________________________________
>> 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
>

You can also use
select all;
set fontsize 18;
On 10/10/25 2:47 AM, Francesco Pietra wrote:
> Hello
> Is any command to change the size of labels for all atoms at once?
>
> I have such a request by a referee about a submitted paper, as he 
> wants to see the molecule better. Displacing the labels is not enough
>
> Thanks
>
> Francesco Pietra
-- 
George Lis...@be...
Chemistry Department 608-363-2225
Beloit College
700 College Street
Beloit, WI 53511
Robert H. Solem Emeritus Professor in the Sciences
http://chemistry.beloit.edu/classes/lisensky

Just zooming the molecule changes the relative size of the labels.
Try this:
load $glycerol;
background white; color bonds gainsboro;
select carbon,oxygen;
label "%[atomno]"; set labelalignment center;
font label 20 bold; color label yellow;
---------
Then zoom it with mouse wheel.
JOhn K.
On Thu, Oct 9, 2025 at 11:48 PM Francesco Pietra <chi...@gm...>
wrote:
> Hello
> Is any command to change the size of labels for all atoms at once?
>
> I have such a request by a referee about a submitted paper, as he wants to
> see the molecule better. Displacing the labels is not enough
>
> Thanks
>
> Francesco Pietra
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>

On 2025年10月10日 09:47:47 +0200
Francesco Pietra <chi...@gm...> wrote:
> Hello
> Is any command to change the size of labels for all atoms at once?
General pattern here is `font label XY monospaced`. Applied in a MWE which
changes the labels to very large, later to very small:
```
$load $pyridine;
label;
font label 30 monospaced;
font label 10 monospaced;
```
Best regards,
Norwid

Hello
Is any command to change the size of labels for all atoms at once?
I have such a request by a referee about a submitted paper, as he wants to
see the molecule better. Displacing the labels is not enough
Thanks
Francesco Pietra

Hi Bob
That is exactly what I need.
Many thanks.
Harry Powell
—
Dr Harry Powell
Structural Bioinformatics Group
Dept. Life Sciences
Imperial College London
har...@im...
Phyre2 Developer
www.imperial.ac.uk/phyre2 <http://www.imperial.ac.uk/phyre2>
Twitter for server news
twitter.com/phyre2server <http://twitter.com/phyre2server>

I think modelInfo is all you want:
$ x = getProperty("modelInfo")
$ print x.modelCount
* 3*$ print x.models[1]
*{ "_ipt" : 0 "atomCount" : 327 "bondCount" : 337 "chainCount" :
 1 "file" : "https://files.rcsb.org/download/1crn.pdb
<https://files.rcsb.org/download/1crn.pdb>" "file_model" : "1.1"
"groupCount" : 46 "moleculeCount" : 1 "name" : "1CRN" "num" :
 1000001 "polymerCount" : 1 "title" : "1CRN" "vibrationVectors" :
 false }*
So I think that is what you need. If for Python via JavaScript, perhaps
using:
info = JSON.parse(Jmol.evaluateVar(jmolApplet0,
"getProperty('modelinfo').format('JSON')"))
would be the most efficient way to get all your needed information.
Bob

Hi Angel
I think that would probably do the job. I need to declare your "fileControl" variable as a global, then it should work.
I'm slightly surprised there isn't a method within JMolScript that would return the mappings, but if I'm the first person to want it, it's not that surprising!
Many thanks
Harry Powell
—
Dr Harry Powell
Structural Bioinformatics Group
Dept. Life Sciences
Imperial College London
har...@im...
Phyre2 Developer
www.imperial.ac.uk/phyre2 <http://www.imperial.ac.uk/phyre2>
Twitter for server news
twitter.com/phyre2server <http://twitter.com/phyre2server>

Hello Harry
If you do the loading from Javascript calling a JmolScript "load" 
command, you could create the control variable in JS storing into it 
each filename and frame number:
var fileControl = {}
j = "1.1";
f = "molecA.pdb";
fileControl[j] = f;
Jmol.script(myJmol, "load " + f);
j = "2.1";
f = "molecB.pdb";
fileControl[j] = f;
Jmol.script(myJmol, "load append " + f);
etc
Or even call those JS from inside JmolScript commands, or create all 
variables in JmolScript, or run them from within JSmol via the Info. 
loadStructCallback
How does it sound?
·
 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/