Dear all,
I'm trying a page with two Jmols using Jmol-JSO. My code is like this:
var myJmol1,myJmol2;
var myInfo = {
height: '50%',
width: '100%',
jarFile: "JmolApplet.jar",
jarPath: JmolPath,
j2sPath: JmolPath + "/j2s",
use: 'HTML5',
debug:
Thanks, Paul
It seems you are right. I was testing several pages successfully until I hit
the
2-applet page. But now the ones that used to work are not working, so I must
have changed something in the file set.
I'll have to check the files from scratch. Let's wait
-
JSmol in
http://chemapps.stolaf.edu/jmol/jsmol/test2.htm
is running fine for me in Firefox 17.0 (Win7)
both HTML5 and WebGL
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> 2) Entering the "mouse selection" mode by using the toolbar icon
> deselects all atoms. This doesn't happen if the popup menu is used
> instead
I see this logical. If I go into mouse selection I am not expecting
to work against an already selected full set. So the previous "select
Yeah, I was just checking that.
I downloaded JSmol.zip this morning and I am getting error in loading
core.z.js
After checking the js console errors, I located many lines that have a strange
invisible character at the beginning of line. I could select one (together with
the next few letters) and
Ok, after sorting out my problems with the JSmol file set, I can now --again--
assert that where one JSmol works, two don't.
This is my test code:
var myJmol1,myJmol2;
var myInfo = {
height: '50%',
width: '100%',
jarFile: "JmolApplet.jar",
jarPath: '..',
j
Ciao Simone
> I support this idea. Also, I remember reading somewhere that
> selectionHalos is supposed to be set ON by default when a file is
> loaded - which in my case actually does not happen when I load from
> the scripting console.
I don't think so. In my experience this has never been
Yes, welcome to Jmol community
Ah, you can also use the atom number for selection:
select atomno=3, atomno=5;
with may be shortened as:
select @3, @5;
Maybe you like that. AtomNo is sequential from 1 by order in the file
Yes, welcome to Jmol community
Ah, you can also use the atom number for selection:
select atomno=3, atomno=5;
with may be shortened as:
select @3, @5;
Maybe you like that. AtomNo is sequential from 1 by order in the file
Ok, today testing two applets with a simpler design (all in pixels, two
independent Info's, default consoles). Still no success.
I just downloaded a new jsmol.zip
Also a copy of Bob's test3 page (works fine from StOlaf)
See http://chemapps.stolaf.edu/jmol/jsmol/test3.htm
Running it in a local we
Today
http://chemapps.stolaf.edu/jmol/jsmol/test3.htm
is broken, both there and when I download it and test with a fresh download
of the jsmol.zip
The left-side JSmol does not display but the yellow titlebar. The one on the
right is OK
Firefox and Chrome, Win7
With files updated today:
Yes, "color label" is now working for me. Thanks.
> > move 30 0 0 0 0 0 0 0 2;color background black
>
> also worked fine. Maybe you have older files or I'm not getting the right
> ones to you.
Yes, it is working now (no errors) but without the animation effect, just
Hi Rolf
Bob will know what this means, but I'm curious: why the parentheses
after label?
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Ah, I read label as an atom propery, not a function.
:)
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Hello Smith
I have little experience with php, but I will tell you what you can
do with Javascript and hopefully you can adapt it:
> jmolButton("model NEXT","Next")
>
> I need call some php function and together use "model NEXT", when I
> push the jmolButton.
> Can you writ
Pino,
I suggest to first be sure that you clear your browser cache -- js
files remain there and you might be seeing the effect of a mixture of
old and new files
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No idea
But my server was giving me trouble serving some pdb and mol files. Maybe
it's related. I could fix that by renaming to .pdb.txt or .mol.txt (this was
with a
former version of JSmol, I have not checked lately)
The error was in the form of garbage characters in red font inside the JSmol
Simone, the command is "load data"
follow that in the documentation
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Hi Otis
Yes, that's one of the candidates
http://biomodel.uah.es/en/DIY/
It's been some time since I last tested it
For comparison (but not up to date):
http://biomodel.uah.es/en/DIY/comparison.htm
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Yes, many Javascript libraries involvedin Ketcher -- things may get
complicated.
@Philip:
The design of Ketcher interface is not very flexible -- I don't like
much these systems whose functionality relies on "modern html"
(javascript, html5 canvas, SVG) and yet rely on a fixed-size
interface
Hi all
I have an image echo. It's working at its full size, but now I need to
(conditionally) reduce its size. The doc says this is possible using a scaling
factor option in font size. However, I am unable to male it work:
set echo formula 0 0;
font echo 22 sans plain 0.75;
set echo image "ret
Ok, solved it using
set echo scale 0.75
I found that using Google, at
http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm
number 10
However, the doc should then be fixed since it says otherwise
http://chemapps.stolaf.edu/jmol/docs/?ver=13.0#font
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Hi
I have some long scripts running (from spt files) in a JmolApplet within a
webpage.
I would like to include buttons in the page that pause and resume the running
script.
Pause works, but resume seems to be impossible to achieve from the page
(it works from the applet's console).
I have tr
Hi Rolf
Since labels are attached to atoms, I think this is the way it works. When
atoms are not visible, labels go off.
Still, I think I have some trace-only models with labels. I will need to find
out.
An alternative could be to use 3D-attached echos.
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minimization...
How about spinning? I am seeing that at least "quit" does not stop
spinning. Permanent spinning is irritating to me, so I'd be happy
that it is also stopped by one or
> in Jmol app !quit does stop spinning. Also in HTML5 and Java applet.
> Maybe you have an older version?
No. I've being typing quit, no !quit
Now I see, !quit does stop spinning. Good!
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Hello
I think that using Jmol for just displaying several 2D structures is overkill.
>From your MOLfiles many pieces of software can offer a display. For
example, JME is much ligther than Jmol. Or you probably should try some of
the html+javascript based viewers that do not rely on Java.
Readi
There are a few 2D viewer applications that could be used to display
the MOLfiles as flat structure images.
For example, ChemDoodle WebComponents may well do it:
http://web.chemdoodle.com/installation/download
http://web.chemdoodle.com/tutorial/2d-structure-canvases/viewer-canvas
-
@LMH,
see for example a simple demo of table with images of structures generated
on the fly from MOLdata:
http://biomodel.uah.es/en/DIY/ChemDoodle/2d-viewer_4.7.0/test1.htm
That should be easy to connect to whatever you use to generate the html
page and table, right?
-
Bob:
It's ChemDoodle Viewer -- simple enough, and small js files. Not interactive
at all. It reads the MOLfile data which seems to be what is available for LMH.
LMH:
You will have to read the documentation available at the ChemDoodle
WebElements website. There are a lot of choices for controllin
Hello Wayne
I've done something of the sort in one of my tests.
Don't recall the exact details now, but it was along this line:
The output "console" that rolls many text lines during initialization
is defined in the "Info" object, by default it is located in the same
position where the JSmol go
> glad I asked because I would have been somewhat stymied by the link
> on that page at the wiki that does not let one download a functional
> version.
Wayne, can you explain that? Which is that link? I can fix it
--
Hello,
I am running several scripts in pages using JSmol (downloaded on 21st
Dec.). Those involving "draw" commands are raising a series of alerts.
I guess it is some debug commands left over in one of the JS files.
For example,
draw pep45 scale 1.2 color yellowTint (4:B.CA) (4:B.O) (5:B.CA) (5:
Hi all
While working on an updated version of "export an image from Jmol applet"
that will be compatible with the new Jmol-JSO method and applet
surrogates, I see that the "image" fallback alternative is not working at
http://chemapps.stolaf.edu/jmol/jsmol/test2.htm
On the other hand I cannot f
OK. I was trying to cover all known variations.
Interestingly, I found that by loading a PNG+Jmol file (saved from the app)
instead of the PDB file, when I specify "image" as the only option in Info, the
png image is indeed displayed. Nice!
Dear Bob,
Thanks for the comprehensive summary on the state of Jmol applet and
JSmol.
First of all, a huge thanks for the tremendous effort you have put in such a
short time and the extraordinary product you have achieved to make. We all
owe you much.
A few notes of my own to share with users
OK, so I have an update of my former "Exporting from Jmol applet an image
of the current view" method,
http://biomodel.uah.es/Jmol/export-image/
that is now compatible with Jmol-JSO-HTML5 (JSmol), Jmol-JSO-Java and
Jmol-JSO-WebGL
it is temporarily located at
http://biomodel.uah.es/en/noJava/exp
> I have not had any problems with this, at least with Firefox. I think what
> you say is true for MSIE.
> It's also possible that I set some sort of flag to allow that.
No, seriously. I'm using Firefox and the JS libraries do not finish loading
from
local files. I gave up trying to understand
Thank you, Pino
I thought that was updated to the last version, but maybe not. I will check the
files again.
I did have some problems loading some pdb files that gave
format-not-recognised errors. I played a bit with file extensions and gzipped
or not, so I may have it broken.
Right now, both h
Quick question:
Can the (recently implemented) pop-up menu in JSmol be
disabled/enabled?
It would be good to have that feature and, if possible, to use
something similar to the applet method, i.e. "set disablePopupMenu
TRUE" in script
Another choice would be some tag in the Info variable
I'll share my experience in Windows on this issue:
Today my Firefox also started blocking the Java plugin I had.
After an update from java.com, the plugin is not fully blocked but
Firefox is asking for permission to run each instance of Jmol applet
(unsigned) -- at least on first use of that app
Hello, Henry
Yes, that is becoming a nuisance.
For me (Windows), although copy does not work, selecting the text and
dragging it to a text editor works, depending on the precise text editor
(cannot give a rule for them, even Word may accept the drag).
A colleague using Mac reported this procedu
Dear Eric, glad to hear from you
> In Windows 7, I find huge speed differences between browsers for
> JSmol. Sorry if this has already been reported.
I am also seeing this, although I haven't done a systematic analysis.
I understand all comes down to the Javascript engine or
implementation of
, I am a Jmol user, and I am not comparing Jmol to
> this or that software, but it seems that Jmol would adopt canonical
> selection rules that coincide with the PDB formatting style.
Is the segid in the PDB specification? I never saw it
·
Dr. Angel Herráez
Biochemistry and Molecular Biol
Hello again
I suspect this is an issue of different terminology, but the functionality you
ask for is likely there.
Some pointers:
http://chemapps.stolaf.edu/jmol/docs/#atomexpressionsfunctions
see WITHIN SEQUENCE
e.g.
select within("PGATG",*) //would select all atoms in that peptide sequence
Hi
So this is a question of file format.
PDB file format specification has not any hint of columns 72-75 or the segID
field, either in the current Version 3.3: July, 2011 / Nov. 21, 2012
http://www.wwpdb.org/documentation/format33/sect9.html#ATOM
or in the oldest referenced in wwPDB, Version 2.
I'm pretty sure I can help you out, Eric, but not right now. You'll
need to give me some time.
First shot: have to tried to wrap the jmolApplet() call in a div that
has style float?
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I'm pretty sure I can help you out, Eric, but not right now. You'll
need to give me some time.
First shot: have to tried to wrap the jmolApplet() call in a div that
has style float?
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Egon, does that depend on whether your tablet is in landscape or portrait
orientation?
I'm just curious...
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An what about JSmol? Will it run in the Nexus web browser?
I am reading it's got Chrome -- it should run!
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The release notice for Firefox 18.0.1 includes this line:
- Faster JavaScript performance via IonMonkey compiler
good for JSmol !
and
- better image quality with our new HTML scaling algorithm
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I found this. It is not the same, but related
Prototype/reference implementation for encoding and decoding atom serial
numbers and residue sequence numbers in PDB files.
The "hybrid-36" counting system.
http://cci.lbl.gov/cctbx_sources/iotbx/pdb/hybrid_36.py
---
Hi Pino
Nothing to do with my site or with Jmol/JSmol.
It's an issue of Java version and browser version and policies.
Nasty indeed. Anyway, for me once I accept the alert the applet loads fine in
Firefox 13, IE 9, and Chrome (Java 1.7.0_11)
And the JSmol boxes should be working fine, right?
O
Mike, I downloaded it like 2 hours ago and it unzipped well
(Windows, WinZip)
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Hi Jonathan
I don't think that download or ftp will be your problem. It is a
zipfile, so the contents will not be altered during file retrieval.
Make sure you are downloading the correct file,
http://chemapps.stolaf.edu/jmol/jsmol.zip
Then it might be a question of how it is unzipped, but I woul
> http://myweb.brooklyn.liu.edu/jgough/ChemResources/example3.htm
I am not sure, but it is possible that this line within Info in your page
j2sPath: "j2s",
is read as "find the files in subfolder j2s of the current (i.e. this page)
folder"
So it's no surprise that it does not load
I think you
Hi Jonathan
I have no experience with MO, but some with surfaces.
Although you can include color and translucency in the same surface
command, I' ve found it tricky and the safest is to do it separately. You must
give a name to each surface first. Try this:
isosurface surf1 mo 6;
isosurface su
> I find that Java 7 (1.7.0_11) on Windows is very sluggish. So slow that it
> could well drive away
> most users of complex Jmol pages (e.g. Proteopedia, FirstGlance in Jmol).
That's strange, Eric.
I've been using Java 7 for a long time in one of my PCs and have not noticed
this problem. It mi
In Windows, since a week or so when this Java "danger" started, Firefox
blocks all applets but allows you to activate them by one click -- until next
time a page is loaded, then you must do it again.
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> Thanks. It seems to be working now for me.
Great! And the solution was...?
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Hi David
I'm afraid I have no experience in building apps, but as a first line of attack
I'd
ask: is this problem restricted to the use of 2 JmolPanels?
To me it seems indeed that the path is not being properly parsed and you get
a mixture of the base path + the chosen path.
Another thng to tr
There's probably no updated API documentation written anywere
Bob may tell you for sure what's the state, or towhat extent you can keep
using the old one.
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Hi David
I don't know about doing this at the development level, but with scripting he
regular app or applet:
xyz format does not provide connectivity (bonds)
mol format is also quite simple and does include bond information
---
Simone, do you have a url we can test?
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Hi Jennifer
http://sourceforge.net/mailarchive/forum.php?forum_name=jmol-users
is the official archive, but I agree there is no apparent way of
searching through it
There are several mirrors, e.g. I regularly use
http://www.mail-archive.com/jmol-users@lists.sourceforge.net/maillist.
html
that ha
Dear Jmolers,
You may be interested on reading this -- it is offered for free by ACS
Interactive Web-Based Pointillist Visualization of Hydrogenic Orbitals Using
Jmol
Shane P. Tully, Thomas M. Stitt, Robert D. Caldwell, Brian J. Hardock,
Robert M. Hanson, and Przemyslaw Maslak
J. Chemical Educati
Hi Tony
As the test report says, Safari should be compatible. The most likely cause
for your problem is recent policies of blocking Java applets due to the
vulnerabilities reported. In particular, Apple remotely forces applet disabling
in Safari.
I'm not a Mac user, so I cannot offer specific a
Hi Bob
> We had some problems with MSIE 9, but that should be fixed. If someone would
> try this with
> Safari 5.1, I would appreciate it. Particularly the link down on the middle
> column, load k04041.cif
> {1 1 1}
> http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
Works in Safari 5.1.7 (Wind
Dear Eric,
I cannot reproduce your problem.
> Fixing the monitor line with the mouse also fails at
> http://chemapps.stolaf.edu/jmol/docs/examples-12/simple.htm
> (Jmol 13.1.11 signed applet).
That works correctly for me. I can set monitors for distance and angle using
the mouse.
Firefox 18, W
This feature sounds interesting. Simplistic protein rendering! :-)
> I think you are suggesting:
>
> ellipsoid {atom set}
>
> Should we give that a try? Oliver, would it be useful to allow an
> option that includes atomic masses?
I had a request (off-list) recently as to how to find the center
El 13 Feb 2013 a las 18:00, Eric Martz escribió:
> This restructuring of FirstGlance HTML was
> greatly facilitated by the "resizable Jmol"
> template B generously provided by Angel Herráez
> http://biomodel.uah.es/Jmol/resizable/inicio.htm
> I am deeply thankful to A
Jonathan, I'd say that has nothing to do with JSmol but with server
configuration.
I saw that for JSmol pages, being all js loaded into the browser, gets a
different behaviour than with Java. For example, from my server the
extension also raised different behaviours when loading (I don't rememb
I agree with Otis regarding the use of txt. I still try to avoid using txt
systematically (beacuse I quite prefer to know what's in a file) but it may be
a
sensible mesure.
> Served file suffixes have to be registered. I don't understand why this would
> be browser
> dependent, however.
Well
> If a file is a binary type, some browsers simply won't be able to
> read it ever from your hard drive. But they will from a server,
> provided you have the jsmol.php file installed there, which will
> convert the binary file to BASE64 and pass it back to those
> binary-incapable browsers in t
Hello Simone
#1
I believe (but am not sure) that with the latest versions you only
need to call JSmol.min.js
The call to j2sjmol.js will be done internally based on the path
specufied in the Info variable.
#2
Information in the Wiki is not up-to-date (must find time to do it,
and the WIki was
Ah, OK
JSmol distribution is still not well roganized, I'm afraid. There's
also a bit of confusion between Jmol-JSO and JSmol (which I'm
planning to sort out and explain in the wiki)
I suggest that you download from StOlaf. The link is in the wiki
http://wiki.jmol.org/index.php/JSmol
(there us
Robert Hanson wrote:
> draw scale 500 arc ... 5-Angstrom diameter
500 ==> not 5 angstrom, I'd say ?
> * What's the best way to draw a line without an arrow head? Use 'draw
> cylinder'?
> Yes, I think so.
There is "draw line" (polyline) and "draw curve", which is useful e.g. for
arbitrary cu
On 23 Feb 2013 at 15:36, Robert Hanson wrote:
> with unreleased updates going to
> http://chemapps.stolaf.edu/jmol/jsmol/jsmol.zip
That should be
http://chemapps.stolaf.edu/jmol/jsmol.zip
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s when you mean angstroms, to be
sure.
>
> BTW, these behaviors are still present in 13.0. Thanks for updating,
> Andreas.
>
> Thanks,
>
> -Spencer
>
> On Sat, Feb 23, 2013 at 3:38 AM, Angel Herráez
> wrote:
> Robert Hanson wrote:
>
El 24 Feb 2013 a las 20:29, Robert Hanson escribió:
> Anybody know if that's the case? -- That if you access your local
> machine via localhost and an apache server, you can access files that
> are not downstream of the path of the HTML page?
I'm not sure right now if in my case the paths resemb
> right -- let's get that clarified on the wiki.
OK, I will do it.
Still I cannot grasp what is the exact limitation, all being
javascript any folder should be possible. We are not talking about
getting files from other server.
On 25 Feb 2013 at 13:27, Fred Ziegler wrote:
> All:
>
> Uploaded to the serverFEZtest5.html (subdirectory), and JSmol and
> cyclohex.mol to the directory, one level up). Does not work. Used ../
> annotation in three locations. What am I doing wrong. Fred
Fred, I tried your source code local
> When is a bug not a bug?
I guess it depends on the number of legs it has :-D
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> http://biology.kenyon.edu/BMB/biomolecules_jsmol.htm
Working for me , too
(Firefox on WIn7)
Clear your cache, maybe
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Dear Jmolers,
Information about JSmol and Jmol JavaScript Object is more or less
complete and up-to-date now in the Wiki,
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object
More details will be need to be added later, but I believe this now agrees with
the current state and, even if not comp
> http://biology.kenyon.edu/BMB/jsmol/simple2.htm
Yes! Same result as Mike: first it loads the Java applet, but the HTML5 links
loads the JSmol version OK
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I am hitting my head against the wall. Cannot trace what's going on.
Can this error be due to location of files and folders?
Error: TypeError: b._script is not a function
Archivo de origen: http://localhost/jsmol_28feb/JSmol.min.js
Línea: 289
It's happening with both Jmol.Java and JSmol.HTML5 usi
Rolf, you can check out
http://wiki.jmol.org/index.php/Protein_Community
Hope it is correct
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Hi Richard
That error usually displays when the applet JAR files are not found,
either because of a wrong path or because you specify signed applet
and have only the unsigned files (or vice versa).
I don't think it has anything to do with Java policies. Maybe because
of the blocking dialog the b
I would say:
1. you need an envelope div#1 or other element that has position:relative
(absolute will do too)
2. inside that div#1, you set div#2 with position:absolute; left:0;top:0;
3. inside div#1 and next (sibling) to div#2, you set div#3 also with
position:absolute; left:0;top:0;
div#3 wil
Based on current (generated) source code in
http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
this could be enough (portions in red added over the existing code):
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> I can see how we might want two different images, one first and then one
> during loading. A nice
> animated GIF would be handy for the loading part.
My previous tests (but not with current JSmol) showed that the browser
cannot cope with animated GIFs while loading JSmol libraries. They just
Greg, this sounds very interesting. I hope you can succeed.
> I have successfully included JSmol in our VLE pages
It would be interesting to the Jmol community if you could share some
guidance abbout that implementation. There is a section in the Jmol
Wiki,
http://wiki.jmol.org/index.php/CMS_
Otis, have you tried
show PDBHEADER
?
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Olá Sérgio
This problem comes back from time to time, I thought we could be
forgetting it.
All depends on whether the browser knows the encoding of the
JavaScript and JmolScript files.
You are using the Java applet, not JSmol, right?
First choice I would suggest is to make sure that all html
El 11 Mar 2013 a las 9:04, Sérgio Ceroni da Silva escribió:
> Already tried that using Notepad++, encoding in UTF-8 with and without
> BOM. No success.
m... Weird
Do you have a link url I can see?
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Richard, my experience is that IE behaviour changes dramatically depending
on the (compatibility) mode it adopts --particularly for CSS-related things.
For
that, including a proper DOCTYPE in the page header is crucial.
But I'd expect IE8 to work correctly for most things also in JSmol.
-
That's great, Bob
Users: you may be also interested on my tests along this issue:
http://biomodel.uah.es/en/noJava/export-image/index.htm
Maybe it's the same technique Bob has implemented.
Note that page is not using the latest JSmol files.
Server-side processing is only needed for IE clients.
Hello, gridbird
Welcome to Jmol!
#1
> now I am wondering that is there any example in which the applet
> window size can be adjusted by mouse
The applet may be resized by javascript commands; mostly you could
use
http://jmol.sourceforge.net/jslibrary/#jmolResizeApplet
But the example you sh
> Thanks for this Angel. As far as I know the only HTML5 definition is
> :
> .
I agree. And that makes our life easier.
> I tried my testpage
> http://www.biotopics.co.uk/jsmol/glucosetestcutdown.html recently
> with IE7 on an old machine and it did not bring up the image.
Yes, my copy of IE
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