> With all the other power in Jmol, it seems reasonable to me that chains
> could be renamed.
It is my understanding that features like chain ID, residue name and number
are hardcoded at the beginning, when the pdb file is initially read and parsed,
and cannot be reprocessed later. (Based on so
John,
The console in the application has a "font" button at the bottom that cycles
through several sizes.
The popup menu is fixed, I think.
If you use JSmol inside a webpage you could control font sizes via added
CSS rules.
Hi Chris
It's a long time since I looked at x3d export.
Is this happening only with that particular file?
Have you tried exporting to VRML, and see if the problem is the same?
Those would help for diagnosis
--
Attend S
I think the problem is cartoonFancy -- maybe not supported for export
I have just produced some X3D for that model without that
--
Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
Francisco, CA to
Hi Chris
All the ways you mention should be equivalent, since in the end they run the
same command.
>From your description, this is a bug in the newer version(s) of Jmol. For
whatever reason it seems to appear only for certain models.
I cannot help with that, but Bob will surely track it down.
Hi Chris
I can confirm the error.
http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
(JSmol 14.6.0)
load 1hho from RCSB
popup > File > Export X3D
in Chrome, Win10: two dialogs for file save, and finally an undentified
network error (maybe a timeout?)
in Firefox, Win10: two dialogs, successful down
> OK, this observation makes perfect sense. It turns out that when you use
> cartoonsFancy (or
> "cartoonFancy"; they both work, because I got so tired of not remembering
> which it was...) a
> variable doesn't get reset after the file is created (which is written OK,
> right?) and then the sc
Hi Rick
a few comments:
1. I can recommend that you try PovRay output. It is PNG, transparent
background and much better look. You don't need to learn how to use
PovRay, producing the images is straightforward. You have to install
PovRay, export to PovRay format from Jmol and then save from Pov
Dear Bob
I will likely get involved on this.
For now, just two quick comments that popped up:
1.
I have had big trouble running my pages locally since I moved to JSmol. That
may be due to them being old and ellaborate, with a combination of folders,
pdb or mol files, scripts, common JS files.
Sure!
The question is... where to locate it?
Goes to the to-do list. Suggestions or actual page edition are welcome
On 8 Jul 2016 at 9:59, Robert Hanson wrote:
Might be a nice addition to the Wiki.
--
Attend Shape: A
Dear Jmol users
I have defined a shortcut link to Jmol Scripting Doc, for convenience:
http://bit.ly/JmolDoc
leads to the Jmol Scripting Documentation page at StOlaf
Feel free to use and share it if you wish
--
Chris, the problem is possibly that PNG data is binary, while X3D data is text
I am not sure you can put binary data in a javascript variable. So the
limitation might be in the js side rather than the Jmol side.
--
W
Chirs, please hav a look at "getProperty image"
under http://chemapps.stolaf.edu/jmol/docs/?ver=14.6#getproperty
It's only defined as JPEG but does the trick
·
Dr. Angel Herráez
Biochemistry and Molecular Biology,
Dept. of Systems Biology, University of Alcalá
E-28871 Al
The question is
Does Windows 10 on a Surface Pro 4 support Java?
(I have no idea)
El 14 Jul 2016 a las 8:19, Matthew Staab escribió:
>
> Can Jmol be installed on a surface pro 4 running windows 10? I have been
> unable to do so.
>
>
·
Dr. Angel Herráez
B
El 14 Jul 2016 a las 12:13, Robert Hanson escribió:
> Note that by putting a PNGJ file into a variable you can
>
> -- extract or exchange the image
So a question would be,
How to apply that extracted image in the page, e.g. as the source of an
tag created dynamically in Javascript?
--
load ==RAP
and you have it!
Of course, you can browse the different proteins to check the actual "real"
3D structure they bind
·
Dr. Angel Herráez
Biochemistry and Molecular Biology,
Dept. of Systems Biology, University of Alcalá
E-28871 Alca
a little fun: browse rapamycin structures at PDB:
http://biomodel.uah.es/JSmol/rapamycin.htm
--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which
Sorry, something was preventing models from loading --only in some
browsers.
I have changed to a newer Jmol version (14.6).
Please force reload of the page and it should work now
> > a little fun: browse rapamycin structures at PDB:
> >
> > http://biomodel.uah.es/JSmol/rapamycin.htm
> >
---
Hi Eric
I agree it's a bug. I would expect both models to be saved, and the doc says
"Only the currently selected atoms are saved."
If you save to SDF it works as expected.
The fact that the file has MODEL ENDMDL means that Jmol is indeed
intending to save both.
So for proteins, you could instea
Hi Eric
I agree it's a bug. I wuld xpect
--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most ban
Dear Bob, that makes sense. I did not realize.
Additional problem is that saved pdf file (with 1st model empty) cannot be
loaded back into Jmol, it hangs with the spinning cursor forever.
--
What NetFlow Analyzer can do
Dear Eric,
This seems to do the trick:
print {*.CA}.sequence.join("")
also
print {*.CA}.group1.join("")
A more verbose version:
t = "";
a = {*.CA};
for ( i=0; ihttp://sdm.link/zohodev2dev
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Hi Tom
All looks good, but I am not familiar with the GWT environment. There might
be some confilct.
One question: When are you calling that code? Is the "myContainer" node
already created?
The error is not helpful, but you could try defining the variable at the
beginning (head section) as
I have had a little practice using Augmented Reality using a downloadable
piece of software --by Colin Berry-- and molecular models exported (VRML)
from Jmol:
http://www.cf.ac.uk/biosi/staffinfo/berry/AR/ar.html
doi:10.1002/bmb.20805
You need to run the software in the computer you want to use (Wi
Hi Henry
Apart from sorting out your missing css file, this is my advice:
1.- You probably should get rid of your frames (although I have always been
an advocate of frames when they provide functionality) Additionally, your
frames definitions have inconsistencies: 69%, 65% 65% -- I do not see th
Henry,
Please see attached template page.
The following section of this message contains a file attachment
prepared for transmission using the Internet MIME message format.
If you are using Pegasus Mail, or any other MIME-compliant system,
you should be able to save it or view it from within yo
Hi Vin
Can you explain more what you are after?
I know Dspace only as something related to libraries, either a way to store
references or full articles (not sure now)
JSmol files are stored in any server that is holding webpages with models.
What kind of application or use are you thinking of?
Hi Chris
Nice product idea
When you say it's free, do you mean I can get a final quality image? The
interface just says "order" -- will one place an order and get the image
without paying while this is in beta?
I was missing some real samples.
-
(moving this to the users list)
Hello, Graeme
In principle, yes, it is possible to load the JSmol libraries from a server
different to the one that hosts the page.
However, the browsers may impose security restrictions for cross-browser
access in certain circumstances (I don't know the precise de
I am surprised. As far as I know, the jsmol.php is only used for loading
models in binary format (and only for some browsers), not for used to load
the javascript making the page .
Have you tried loading a plain MOL file, for example, or a file from NCI
CACTUS using "load $aspirin" ? That woul
Another problem that looks like a bug:
I am unable to use deferUncover: true,
it has no effect at all, the model loads straight after the image without any
clicks.
This happens both with defaultModel and with a local model loaded via
Info.script
var Info = {
defaultModel: "=
There seems to be a bug when using Info.defaultModel together with
Info.deferApplet
A basic page with the code below
1. displays the image
2. on click, loads JSmol, the loading echo and then the model
3. the model disappears and the loading echo is displayed again
History in the console matches
Thanks, Bob
Sorry for the complaint. It seems I was misunderstanding the use of
deferUncover
> Q: Does https://chemapps.stolaf.edu/jmol/jsmol/cover.htm work for you?
> Q: How do these differ from https://chemapps.stolaf.edu/jmol/jsmol/cover.htm ?
They work the same, yes.
So I was expecting the
OK, I will ammend the wiki to clarify the issue.
But, important: Peter, has this behaviour changed across Jmol versions?
It is one thing that Jmol identifies or not the format, as Bob has explained;
it
is another if there has been a change in behaviour.
Thanks
---
Hi Mathew
Possible sources of trouble (just a guess)
- quotes (particularly when they get nested)
- line breaks
all that related to Javascript handling of your text string
If you could provide a sample as plain text of what the php variable outputs.,
it would help diagnosis.
Another idea: writ
Mathew,
that lacks newline characters apparently. Jmol needs either those or vertical
lines (the 'pipe' character, | ) Try inserting a pipe before each new line·
Dr. Angel Herráez
Biochemistry and Molecular Biology,
Dept. of Systems Biology, University of Alcalá
E-28871 Alcalá
You may also need a space between the pipe and the element symbol, so it
seems
> that lacks newline characters apparently. Jmol needs either those or
> vertical
> lines (the 'pipe' character, | ) Try inserting a pipe before each new line·
---
Glad you solved it
As far as I remember, the pipe character serves the same as your \n
Inline loading is always tricky!
On 26 Sep 2016 at 12:49, Matthew Kennedy wrote:
Thank you Angel, in the end, it appears the issue was that it needs to print
out the literal \n's
in the script line. So t
Re: revised VRML output and new STL output
Congratulations, Bob
I understand this means a change in the VRML output starting with this
version. Something worthy to make a note, just in case.
Question: what is the status of the X3D export? As far as I remember it was
written by matching the V
> The text field would be a solution but a functional menu would be better.
The menu is managed by jQuery-UI
so the fix should come from there. I guess there is some mobile-friendly
jQuery
Jmol users
Maybe we should raise funds to buy Bob that iPad !
crowdfunding is the fancy word now
;-)
Hi Thomas
Probably the easiest way:
1.- Define you Info variable with
width:"100%",
height:"100%"
2.- Wrap your source JSmol, as well as your target JSmol, in a DIV and set
their size via CSS.
JSmol will always fit the wrapper div, which you can easily resize via css and
Javascript
---
El s
Dear Kuntal
That should not happen.
Please provide details:
- version of Jmol you are using
- the Jmol state of you model as you want it rendered -- you can save that
usingwrite state "filename.spt"and send us the file, so we can test the
PovRay export
-
I can confirm what Kuntal was reporting, and also with a different model
So there is a bug
in PovRay export from Jmol 14.6.4_2016.10.21
Atoms are rendered much bigger. Bonds seem unaffected.
See example:
PNGJ made by Jmol (alanine from NCI):
http://biomodel.uah.es/angel/Jmol/Ala.Jmol.png
Hi Jonathan
#2 confirmed, with 14.6.4_2016.10.02:
load $caffeine
getproperty moleculeinfo // reports moleculeinfo[1].nElements 4
load $caffeine
getproperty moleculeinfo // reports moleculeinfo[1].nElements 8
...and so forth. Every new load increases that by 4 -- cumulative
initiliaze does no
For the record:
This has been fixed for the next release, per revision [r21288]
https://sourceforge.net/p/jmol/code/21288/
--
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Access to Intel Xeon Phi processor-b
Will this affect Jmol functionality?
e.g. loading files from PubChem
"NCBI will begin redirecting all HTTP traffic to HTTPS on Thursday,
November 10 at 9 AM EST (2 PM UTC)"
https://www.ncbi.nlm.nih.gov/home/develop/https-guidance.shtml
Hi Doug
Have you tried to add a manifest to your zip file?
According to
https://chemapps.stolaf.edu/jmol/docs/#loadzip/jarfilesandjmolmanifest
that allows to instruct Jmol to load several files within the zip
On the other hand, a quick test I made a zip file with 3 files and without
more preca
Dear Bob,
Well, Jmol does exactly that! When I load a manually created zipfile with 3
files into Jmol 14.6.4_2016.10.02, it loads the 3 molecules in 3 frames.
Additionally, the documentation suggests it will do so, since options are there
to exclude some files or to ignore the manifest:
https://c
Yes, a zipfile made of PDB files fails to load for me too in 14.6.4
It works with files in other formats.
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There's always some way with Jmol ;-)
Please try this:
xx = load("3-pdb-files.zip");
zap;
for (i=1;i<=xx.lines.length;i++) { load append "3-pdb-files.zip" manifest
@{xx.lines[i]} }
That may be easily put in a function that takes the file name as argument, if
more convenient.
---
El software d
Pino, I also see the same error. So this is not a cache issue (my first
thought).
I do not think it has anythng to do with the "load" command, it is previous to
building the JSmol object.
On the other hand, the error may not be exactly in that js file it mentions; in
my experience the error re
Dear Bob:
I am not seeing any difference based on one or several tabs, one or two
Firefox windows. It is running at around 40 ms, most of the time actually
below it occasionally reaching 50 ms
https://chemapps.stolaf.edu/swingjs/phet/site/swingjs/examples/phet/GasPro
perties.htm
Firefox 50.1.0
Hello, Huan
You are in the right drection.
> Actually, I found a very brief introduction in Jmol Wiki website, where
> listed some commands for loading PDB file and
> running script in command line. However, I did not see any command for saving
> data.
Not specifically to save data, but it'
Sorry, I copied the wrong piece of code in my former reply. This is the correct
way:
Hello, Huan
You are in the right drection.
> Actually, I found a very brief introduction in Jmol Wiki website, where
listed some commands for loading PDB file and
> running script in command line. Howeve
onds ({2 3})
Should that work as such?
·
Dr. Angel Herráez
Biochemistry and Molecular Biology,
Dept. of Systems Biology, University of Alcalá
E-28871 Alcalá de Henares (Madrid), Spain
--
Developer Access Progra
Thank you, Matt
Further testing indicates that he command itself is working as it used to be.
Suspicion is now on a possible change in the way bonds are indexed,
between old PDB files and recent mmCIF files
(this is in Proteopedia which changed the source of files last year)
---
El software d
Yes, that seems to be our issue. So we need to redo the state scripts.
Thanks
On 13 Jan 2017 at 18:07, Robert Hanson wrote:
Ah, yes! bonds are indexed COMPLETELY differently -- and are not even the same
set of
bonds -- in PDB, mmCIF, and MMTF.
---
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Hi Max
Two issues here. One is the way to achive this in Jmol scripting. The other is
to specify what you are expecting to achieve, i.e. which is your criteria of
bond ordering + coloring.
Atoms are indexed as the file is read, and so there is no issue: they receive a
sequential number and you
Hi Max
Have you explored the "connect" command?
>From your last description, I think that might do what you want.
It's easy to select atom pairs by distance, and then you could "reconnect"
them and apply color and thickness of bond
https://chemapps.stolaf.edu/jmol
Dear Jmolers
I'm trying to set an echo that will display after a minimization has finished.
I prefer not to apply single thread "using set useMinimizationThread false",
so I thought I could us the callback,
but I am unable to make it work
Does anyone have a working example?
This is what I've tr
XYZ files do not include bond information, while MOL and MOL2 do.
So I guess your C--P distances are above what Jmol considers "bonded"
Maybe you can change the default value of
set bondTolerance (decimal)
"When autobonding, the value of bondTolerance is added to the two bond
radii of atoms being
Thank you, Rolf
Yes, it seems that although the callbacks can be targeted to a jmolscript, it
does not allow to pick any parameters like it does in Javascript.
After all, even though I was developing in the Jmol aplication console, my
target is a webpage, so I have "outsourced" the processing t
Hi John
Sure!
You have the width of the standard, flat, ribbons:
ribbons 0.4
ribbons 1.5
(meaning angstroms)
and if you want thick ribbons you need
set cartoonFancy on
set ribbonAspectRatio 12
set ribbonAspectRatio 4
(the lower the value, the ticker is the ribbon)
plus the above width
---
El
Dear Bob,
Scaling fonts in labels is very nice.
However I am seeing a funny behaviour: when I manually zoom between two
label commands, they behave different in size. I checked now and it also
happens with a scripted zoom.
Example:
load $caffeine
set fontscaling true
color label yellow
set labelo
gt;
> set fontscaling off;label xxx;set fontscaling on
>
>
>
> On Tue, Feb 7, 2017 at 5:33 PM, Robert Hanson
> wrote:
> I might be able to fix it. The problem is that you are changing the
> label
> after you are setting its sizing facto
Dear Bob,
I was interested on that new functionality "drag from a url onto the Jmol
application" you mentioned recently.
Is that included in this release?
--
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Hi David
This sounds like something related to loading binary files via jsmol.php
Please check:
1. What format are your model files? ARe they binary? Does the problem
reproduce with plain-text-formatted files (e.g. MOL)?
2. Are you running from web server, or from local disk?
3. How have you co
Ok, those details are useful
It is possible that Chrome has recently changed its security policy (and so it
would not matter which Jmol version you use) regarding retrieving of files via
other browser different to the one the page is in. But this should only affect
binary files, as far as I kno
Hi David
When I go to
http://hibbitts.rc.ufl.edu/tour
The (methanol) model loads correctly both in Firefox (Jmol-Java), Chrome
(JSmol-html5) and Edge (Jmol-Java) (all in Win10)
I also notice that it is running Jmol 14.4.0 from 2015, both Java (Firefox) and
JSmol-HTML5 (Chrome)
So the
And regarding these worries...
> The tmp.aI5qUbCWPc folder changes (it's randomly generated) and I'll be careful that it doesn't
> coincidentally collide with the above list.
You can redefine and hence override the variable used by Jmol, to always
avoid binary handling
add for example
Hi Richard
I have a lot of pages that have been evolving alongside Jmol changes.
I see no reason why "the Jmol applet-based stuff will not be convertible". Can
you explain?
I've converted all my Jmol applet pages to JSmol, and first I set them to use
Java by default, or based on identification
Dear Jmol users,
You should be aware that Firefox
has joined the trend to abandon Java
applets and the latest release can no longer run Jmol in pages. Of course,
JSmol-html5 is perfectly functional. Google Chrome and Microsoft
Edge are
another 2 major browser that cannot run Jmol-Java.
Fi
Hello Bruce
I will gladly take a look at your page when I have time, but here are a few
comments in advance:
1. Using JSmol-html5 with IE is very slow, indeed. Other browsers are
recommendable.
2. Given the current state of Java support, you'd better forget chances of
using Jmol-Java. I agree
Dear Bob, if we can confirm that, if would be wonderful.
Many of my pages no longer work in local, i.e. when run from local files
(some undecipherable JS errors prevent it; it seems to depend on paths
used and the complecity of the file setup, but I have been unable to pin it
down). I am forced
Have you checked Jmol's "navigation mode" ?
As far as I remember, it used the keyboard.
But maybe it is only applicable to the Jmol application.
http://chemapps.stolaf.edu/jmol/docs/#navigate
http://chemapps.stolaf.edu/jmol/docs/#setnavigation
--
(I'm following another thread started by David Hibbitts but this is a different
topic, so I changed the subject)
David,
May I ask what is the information you have regarding future support of Java
by Waterfox?
On 29 Mar 2017 at 15:14, David Hibbitts wrote:
> It's hard to know how much any of us
Hi Nicholas
> However, if I issue the command $calculate structure and then redisplay, the
> structure
> is then shown with a ribbon consistent with DSSP, running from 365 to 373.
> Can anyone
> tell me why Jmol doesn't display this stretch according to DSSP in the first
> place?
I am not
Hi Jaime
It's always been like that by default, but I think there is an option:
set fontscaling on
although it is a little tricky to get it working when there is zoom between two
applications of labels.
See https://chemapps.stolaf.edu/jmol/docs/?ver=14.6#font
Hi Donna
You could probably use
set appendNew false
load append data ..
See
https://chemapps.stolaf.edu/jmol/docs/#set_appendnew
https://chemapps.stolaf.edu/jmol/docs/#loadappend
https://chemapps.stolaf.edu/jmol/docs/#loaddata
https://chemapps.stolaf.edu/jmol/docs/#data
---
El software de
[I'm moving this to the jmol-users list]
Hi Jeff
I foresee no problem in your scripts.
My advice is that you right-click and open the Console, then paste there your
scripted commands one at a time and see which one gives the error or fails
to work.
On 28 Apr 2017 at 15:15, Jeff Sims wrote:
think of this before since you started the discussion with JSmol (or
so I understood). The saving of window settings to a history file only applies
to Jmol standalone application.
·
Dr. Angel Herráez
Biochemistry and Molecular Biology,
Dept. of Systems Biology, University of Alcalá
E-28871
Ciao Luciano
Although Jmol obviously "knows" the screen-Z position of an atom (used e.g
in perspective, fog, slab and depth, rotate best), I can find no command that
will retrieve that value.
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Great solution
I just noted this in the documentation (under "functions"):
point({x,y,z}, true)gives the screen coordinates {sx, sy, sz} corresponding
to
the 3D coordinates {x, y, z}.
point({sx,sy,sz}, false)gives the 3D coordinates {x, y, z}
cooresponding to
the screen coordinat
Of interest on this topic, this article has just been published:
Implementing WebGL and HTML5 in Macromolecular Visualization and
Modern Computer-Aided Drug Design
Shuguang Yuan, H.C. Stephen Chan, Zhenquan Hu
https://doi.org/10.1016/j.tibtech.2017.03.009
---
El software de antivirus Avast
:
http://proteopedia.org/wiki/index.php/Secondary_structure#How_Jmol_Deter
mines_Secondary_Structure
Cheers!
·
Dr. Angel Herráez
Biochemistry and Molecular Biology,
Dept. of Systems Biology, University of Alcalá
E-28871 Alcalá de Henares (Madrid), Spain
Hi Bob
Any chance that I can use "mutate" on a first model when I have loaded two
models (2 files into 2 frames)?
I am testing the different syntaxes from the documentation but it seems
impossible. Some sections do mention "in the last model".
Can you please confirm?
Thanks
---
El software d
Henry, there is some recollection on history at
http://jmol.sourceforge.net/history/index.en.html
which I made time ago from several sources. I cannot guarantee its accuracy
or completeness
Maybe I will move that to a page in the Wiki -- that's an idea
---
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Dear Bob,
Is there a way to extract some residue fron the loaded model and clone or
duplicate it in a new frame/model?
I am trying
ff1 = load('=pdbe/1foz')
load "@ff1"
But I don't know how / if I can extract a subset of atoms from that ff1
variable
(and e.g. create a new model using load dat
Yes, the email looks ugly indeed.
Rather than following the link, I signed in into sf.net, went to user area and
there was a button to renew subscriptions. So it looks perfectly authentic.
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It seems that the result of "contact" cannot be present separately in the two
frames when 2 models have been loaded. Only the latest generated set of
contacts is displayed, and only in the current frame (even if calculated from
atoms in the other frame).
Is there a way around? We would like to
Oh, thanks Bob
I should have known, since contacts are a kind of isosurface! I knew ID is
essential to have several at a time, but I missed that bit now.
This is going to look great!
Thanks
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Callbacks return as their first parameter the ID of the JSmol object (e.g.
"jmolApplet1")
I wonder if this ID could be retrieved directly from a script. I could not find
anything e.g. among the readonly variables
Any hints are welcome
--
Thanks, Bob
> Well, if you wrote the page, you should know, right? ;)
Not necessarily ;-) I mean, applets are generated quasi-automated by some
back-end code.
> All applets are registered in Jmol._applets.
Could be. The problem is to know which of those is involved at a certain
instance.
Al
Thank you, Bob, Paul and Otis
The issue is not easy. Proteopedia has both JS and PHP code that allows
pages to be created by users. So no, I don't always know what is the name
of the particular JSmol object since it is not created manually; they have
sequential ids, but the key is that a scene
Thank you, Henry
I've added your obser vations in
http://wiki.jmol.org/index.php/Troubleshooting/Java_Problems
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Dear Otis
I have seen several files from PubChem that come with more than one
structure, using
load :whatever
So that is the norm rather than the exception. It's easy to browse them if you
load into the Jmol application and use the arrow buttons in the toollbar.
Sometimes, the 2nd or 3rd is m
Hi Jeff
Regarding the font, it should cycle through about 4 steps, coming back to
small size.
I don't know about Mac, but in Windows Jmol creates a ".jmol" folder in the
user's home folder, wher you can see a "history" and a "properties" file.
Try editing them or just delete them and Jmol will c
Hi David
it does look strange.
Have you tried with a former Jmol version?
i.e is this specific to 14.20.2?
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It seems that "rotate" cancels the spin
I have no clue if this has ever been by design.
You could apply a fix by reading the spinning state before doing the rotate
and reapplying it later:
Jmol.jmolCheckbox(myJmol,
"reset;",
"ss = _spinning; reset; rotate x 90; if (ss) { spin on; }"
I agree that reset should stop spinning, but not that rotate also does it
Anyway, there are workarounds by checking the special _spinning variable
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