Hi Steven
You're right; percent does work in FF even in Ohio; especially when
an extra surrounding div block is removed.
Glad you solved your problem.
By the way; your auto
resize template page is great. The code was very useful for
debugging my problem.
Thanks. It's always great
Hi Xibin
I really have no experience with orbitals, but there is a set of test files
within Jmol project.
The URL is
http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol-datafiles/
You can also download a copy for testing from Bob's pages demonstrating
the MO command:
Eric, your question is complex, but for now I have an answer for a part of it:
On 12 Jan 2008 at 17:57, Eric Martz wrote:
However, this solution centers instantaneously. It would be so much
nicer to slide to the new center over a second or so. Can the
moveTo command change the center without
show FILE initial-view.spt
pending
script 8 started
script ERROR: bad argument count
line 2 command 1 of file null:
show file initial-view.spt
Using both Jmol application and JmolApplet 11.0.3, both from local disk
and from the server, show file xx.spt works.
Applets
Romuald,
Since there is no atom where you want, I don't think you can draw a bond. You
can,
however, draw a line between any two points
For example,
I would like to connect the center of mass of an H2 molecule with a
metal center.
assuming those are the only two hydrogen atoms in the model,
Raphael A. Bauer wrote:
background white; select all; wireframe off; backbone off; spacefill
off; trace on;
on a protein with ligands bound to it. unfortunately i am getting the
normal trace plus a trace that seems to connect all ligands (looks like
a giant signature of a MD).
That's
Hi Noel
(1) The link to the wiki on the front page of Jmol is broken
Do you mean the link at the top-right menu? It works for me right now.
The wiki server gives trouble some times, may be that.
(2) Why isn't there something on the front page saying Jmol book now
available? It seems like
On 31 Jan 2008 at 0:03, Nicolas Vervelle wrote:
I know it doesn't work from some places (like my office), because the
Wiki is not on the usual HTTP port (80), but on port 81.
Depending on the security of the place you are connecting from, it may
not work
Nico, would it help if we change
Hello Xavier
Thee is no way to do that currently; labels are fix-size.
But this has been discussed very recently (search the list), and there might
be news in the future.
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Hi Steve
Congratulations! The site looks very interesting. I will come back to you when
I have some
time to play with it.
I find some very interesting approaches there.
At first look, resizing the browser window below 1024x768 is not very well
managed; Jmol
resizes, but the text panels don't
Dear all Jmolers
Prompted by some recent comments on this list, I've thought that Jmol web site
was not too
fit for newcomers, as many important pieces of information were not obvious and
many old
things were rather prominent. In addition, in several occasions I've realized
that people fail
Hi Eric
may that be getProperty appletInfo ?
http://chemapps.stolaf.edu/jmol/docs/?ver=11.4#getProperty
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On 5 Feb 2008 at 16:43, Eric Martz wrote:
Dear Angel,
[...]
Is the Safari behavior a known issue? I see at
http://biomodel.uah.es/Jmol/resizable/ that you tested Safari 2 under
OS 10.4.9 with good results.
I certainly did not test that, as I have no Mac. If the sentence is there, it
was a
Well, I've found a workaround.
Instead of using anim on I do a while loop with Jmol internal read-only
variables and anim next:
set echo top
model rewind
echo Animation going
while ( _modelNumber != _lastFrame )
model next
delay 0.25
end while
echo Ended
Have you tried using a refresh command after the animation and
before the echo?
-Frieda
Thanks, Frieda, haven't tried that... No, doesn't make a difference.
The problem is the echo shows right when the animation is starting. (That is,
the anim
on runs in parallel with the rest of the
Sorry I cannot help directly, but there was a recent discussion on either this
list or the developers, regarding Java 1.7 givng trouble
So maybe it's not a 64bit issue, but a Java one.
Search the lists (they are linked from Jmol home webpage)
HTH
I can cofirm Eric's observation. The problem is with 0% Y
Same happens with 100% X, and it is no longer right-flushed, the text goes
outside the panel even at 95% X. Maybe it's not wrong positioning, but
wrong justification?
It is OK in 11.4.RC5
Both 11.5.7 and 1.5.6 fail
If I remember correctly, Jmol reads atoms without any chain ID as an extra
chain.
This can be questioned, but that's the way it works now
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I'm trying to read an applet size. Right now I'm using
var info = jmolGetPropertyAsArray(appletInfo)
var n = info.htmlName
var iH = document.getElementById(n).height
var iW = document.getElementById(n).width
But I can only use this successfully with pixel-sized
Dear Jmolers,
It's been tough, but after many hours, lots of trial and error, and error, and
error, several
times despair and then a new spark, and much head scratching, I think that I've
found a
cross-browser method for exporting a snapshot of the applet into a page (pop-up
or
otherwise)
Bob Hanson wrote:
Why not just load the model as a full unit cell:
load .pdb {1 1 1}
No?
Yes! I was not aware that could be done with PDB.
I was misguided by sym.htm, which just mentions CIF.
I'm still finding the way to display just the copies I want, but symop seems
to be the
Eran, I think this is what you need:
getProperty appletInfo
appletInfo.htmlName=jmolApplet0
http://chemapps.stolaf.edu/jmol/docs/?ver=11.4#getProperty
You will have to parse the output carfeylly, though. See the appletInfo.txt
linked from there
Eric, I can see what you mean; I've had this problem before with other PDB
files (1GC1).
The problem is in the numbering; the carbohydrate residues are numbered 901,
902,
clustered at the end of the amino acids.
I agree this is undesired, but can't see how Jmol can be blamed for it, or
Hi Janzo
I don't think you need to convert your pmesh into mol or to load any molecule
into Jmol.
Just make it load the pmesh file.
The details may depend on how your insertJmol function is written.
This is what I would do:
onLoad=insertJmol('caffeine_applet',400,400,''); jmolScript('pmesh
Hi, Thomas, welcome to Jmol world!
I can see no reason for the problem you describe.
Try these:
1.- open the Java console* and see if there is some error there
(*find a coffee cup icon in the taskbar, bottom right of your screen,
right-click on it,
choose Open Console)
2.- open Jmol console
Hi Nick
I've seen Bob's pieces of code than can do that.
Basically, you should use connected to select adequate atoms.
There was somewhere a radical definition file with examples of those
definitions. OK, I found it:
http://chemapps.stolaf.edu/jmol/docs/misc/groups.txt
connected is the key
I
On 30 Apr 2008 at 15:14, Nicolas Vervelle wrote:
Does someone know what's wrong with the generated HTML ?
The generated HTML looks OK, and in fact it works when copied locally.
What I see is that, when put in the wiki page, the checkbox-associated
Jmol commands are not being passed to the
On 1 May 2008 at 16:03, [EMAIL PROTECTED] wrote:
From a usability perspective most of what is in the right-button menu
should be in the application menus (and sub menus). The pop-up menu should
be limited to those things that are relevant to being affected for the
item under the pointer at
On 2 May 2008 at 13:37, [EMAIL PROTECTED] wrote:
Mmm, I see Angel. So the app doesn't know it is running as such rather
than as an applet so it can't reconfigure the menus?
In fact, the pop-up menu can be customized, so maybe the top app menu
could be too. The issue is that there has been
Hi Rich
I see your point --more or less--. I gather that you want some more commands
included in
the top menu, and a custom startup set of options. To do that, you'd have to
modify the
source code and package it into a custom Jmol.jar file.
But following your description and comments, I also
Otis, I have no experience at all with Spartan, but as far as I reckon, smol is
Spartan mol.
You have several sample files at
http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol-datafiles/spartan/
maybe the contents of some of them give you a clue
Not really the same, but the MOL2 format
Will future changes made in the old system (downloaded PO files, edited
and uploaded) be copied into this new one automatically, or should we all
move into the new system?
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Hi Frieda
Two quick ideas (untested):
a) I'm not sure if yu can apply coloring togeher with isosurface loading, but
guess you've tried that already
b) There is an isoSurface colorScheme command that may
be applied before loading the isosurface.
HTH,
This seems to work:
1. create the isosurface with
isosurface reversecolor colorscheme rwb sasurface 0.1 map mep
2. save it to jvxl
3. delete the isosurface
isosurface delete
4. load it with
isosurface colorscheme bwr # note that bwr is the opposite to rwb
isosurface Frieda-surface.jvxl
Hi Rajarshi
1. The standard element-id for unknown atoms in Jmol is Xx. You may use that
and select
them successfully using e.g. select _Xx (I've had some trouble with this
syntax before, but
don't remember the final solution; I may search and dig it up if you need so)
2. I'd bet (but
I stand corrected.
It seems that in my previous message I was dreaming; a quick test shows that,
since MOL
format only includes element symbol (and not atom ID as in PDB), Jmol just
converts
anything not matching a known element symbol into Xx. So, you cannot use R as a
symbol.
BTW, you
Nick wrote.
Hi Angel, A very timely contribution. I was looking for a way to
showpositiveand negative
charges on atoms.
A few experiments later I find that
draw {atomno=4} +
draw {atomno=4} -
works quite nicely.
Nick, why don't you use labels for that?
select atomno=4; label +
On 3 Jun 2008 at 16:31, Bob Hanson wrote:
OK -- hbonds, contacts, surfaces -- I need to know what a list is in
Chime.
list in Chime is a script command for a surface. The list is the name
assigned to a surface when created using surface, load pmesh or load
surface gaussian commands. The list
That does the trick.
Now I can display/hide things automatically according to the visibility of
other things.
Thanks, Bob
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Hi all
I've been playing with positioning text in certain 3D coordinates, either using
set echo namedEcho; echo customText
or
draw namedObject customText
They both have strengths and weaknesses. While checking these, one idea has
risen:
Would it be possible to have an option
Hi Nick
Yes, this works for labels as well as echos: use a vertical bar for a line
break
label C|3
Most times you can omit the quotes, but it's safer to put them
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I just found this note in Rich Apodaca's blog:
a piece of software for viewing molecules 3D on the iPhone, including
proteins form PDB!
http://depth-first.com/articles/2008/07/11/3d-molecule-viewer-on-the-iphone
It's some time since I thought about the chances to run Jmol on PDAs and
Hi Nick
Yes, you can save the state:
With the application you can save to disk. The command is
write state
Or, from the menu, File Export State
With the applet,
show state
then copy from the console and paste where you want.
Or from the pop-up menu, both app and applet:
Tom, without testing it, but following literally your message, I'd say you
should try
natoms = {selected}.size;
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Hi David
Anything that can be run from the console can run from a script; there is no
difference.
1hru,A, 12-15, 36-50,
load 1hru.pdb; display *:A and (12-15,36-50)
1hru,A, 12-15, 36-50 and 1hru,B, 59-72,63-80.
load 1hru.pdb; display (*:A and (12-15,36-50)), (*:B and (59-72,63-80))
If
On 23 Jul 2008 at 19:56, Paul Pillot wrote:
I may not understand correctly what your exact need is but maybe the resno
expression does the
trick. eg : restrict (resno26 and resno87)
Exactly; that is the same as
restrict 27-86
Hello Thomas
When using
jmolInitialize(jmol/);
the PDB file is not loaded and the status bar shows Applet
jmolApplet() notinited
Right. Jmol.js does not use JmolApplet.jar, but the set of 16 (?) jar files
which names start
by JmolApplet0. This is recommended since only the required applet
Just after replying, I see now why it may be working in the same folder and not
in the other.
For clarification:
1) If you use
/var/www/html/jmol/JmolApplet.jar
/var/www/html/jmol/Jmol.js
/var/www/html/index.html
and
script type=text/javascript src=jmol/Jmol.js/script
jmolInitialize(jmol/);
Thomas, I see no reason for it to fail.
I have reproduced your example in my local disk and it works both ways.
Two ideas:
1- there may be some problem with the script file: content is not broken,
path is correct, upper/lowercase in the file name
2- Check the Java console to see if some errors
Hi all
After Bob's recent message about implementation of functions for some
toolbar buttons in the Jmol application, today I decided to try a new icon for
the rotate function in the toolbar. So, I am renewing some of the toolbar
icons. Before they are updated for good, I will welcome any
On 26 Jul 2008 at 21:50, Egon Willighagen wrote:
I like the new icons. Might you tune the play/forward/etc buttons too? ;)
Will try, but my artistic talent is very limited :-D
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Thomas Stout wrote:
Very nice. I especially like the new version of the rotate button -- it's
more indicative of 3-d
rotation.
Yes, that was the idea.
I'm of mixed opinion about using the POV-ray P -- if one knows POV-ray,
then they'll
recognize the P, but it conveys nothing to the
OK, so while finding one of the images I discovered a nice set of icons in
WikiMedia Commons. It's got an LGPL licence, so I guess it's suitable to be
included in
Jmol.
So I got involved and made 20x20px versions of the needed icons. I've just
updated
http://biomodel.uah.es/Jmol/toolbar/
Hi Chris
I am not sure, but I recall that there may be a difference between internal
model number and sequential model number in Jmol frame or model
commands.
Check the docs and, in any case, try using number 3 (27 could be 1, first
model, so 29 is 3)
Hi Eric, how are you doing?
I had a suspicion and have just tried it: you can select model=1.1, so:
select all; color atoms translucent;
select model=1.1; color atoms opaque;
does what you want
Oh, and you can also do select model1.5 to get all but the first 5 models
Marvels of Jmol Math!
Angel proudly presents...
Jmol new look!
Now I deserve my summer holidays, having done my quota of Jmol :-)
On 28 Jul 2008 at 13:54, Thomas Stout wrote:
Oh, those are very good! I quite like that set
Kalzium is a periodic table viewer, so perhaps not that confusing?
Hello all
I had this script for getting a projection of certain (dummy) atoms onto the
XZ plane:
{selected}.y=0
this works up to 11.5.41 but gives an error in 11.6.RC4 and RC10
Command expected
Is this intentional, and how can I achieve the result?
Thanks
Hi Dean
Yes. I have used sub in echos, although not often. I have a recent example
using 11.5.41. My echo is Hsub2/subO
Maybe your problem is only with long subscripted texts?
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On 27 Aug 2008 at 10:57, Dean Johnston wrote:
OK, here is the state for ammonia, with a label of Point Group =
Csub3v/sub at the
bottom left. Without the tags the spacing is normal.
Just typing it in the console of 11.6.RC10 app it looks Ok to me
Maybe some combination with other scripts are
Hi Jeff
The key must be in the dump() function, I'd say
You are trying to write an array into a text area. I guess different browsers
may take that differently, unless you force the array to become a string.
Or, how about calling jmolText fully?
document.getElementById(jmolText).value =
Jennifer, thanks for your feedback. I really need it to keep going.
My original plan was to work on volume 2 along this year, particularly during
the summer,
and have it ready for this fall/autumn. But I haven't found much time to work
on it, so it will
be later. Plus, to be honest, the scant
Hi Tom
I'm probably late in joining this thread, but since there has been no final
comment, here's
my 2 cents
1)
Your problem looks to me as more related to a specific browser and JVM that to
Jmol
version (but I may be wrong). Of course, memory is an issue.
2)
i) be able to stipulate the
Hi Jeff
Not sure after the flurry of messages if you have solved your problem.
On 27 Aug 2008 at 16:21, Jeff Hansen wrote:
Unfortunately both off these do the same thing which is to write the
function used to create the Jmol applet object into the into the div as text.
That may be due, as
My previous message lacked a link (I clicked Send too soon :) ):
Have you checked out the method used in Jmol homepage? I'm not sure if that's
what you
are after. A similar solution is what I once called pop-in method for
inserting Jmol applet
upon user request. This is used in Jmol app
On 28 Aug 2008 at 15:59, Jeff Hansen wrote:
Additionally, the alert(result1) (see code below) displays undefined
in the alert box and alert(result2) displays a blank alert box. So
I'm wondering what is going on with that.
I would say that with result1 you are trying to read from the
Hi Jeff
That shuld be in the doc... No! jmolEvaluate is not documented in
http://jmol.sourceforge.net/jslibrary/
Let me take a look at Jmol.js code...
function jmolEvaluate(molecularMath, targetSuffix)
So, you work as with jmolScript. That would be:
var Energy =
On 30 Aug 2008 at 14:20, Robert Hanson wrote:
Jmol 11.6.RC12 now has
set atomPicking [default TRUE]
set bondPicking [default FALSE]
Nice! and quick
Are those 2 independently set, or are they alternative options?
And, how does that combine with the different set picking variants?
(Well, this reply to Henry's posts has become long, so I'm splitting it into
this Chrome-
related part and another Java 6u10 post)
So I've just installed the new Java 6u10RC (1.6.0_10-rc) required for Google
Chrome
It runs.
Bad news: I cannot make any javascript-to-applet work in Chrome
These
(This is a separated thread prompted by Henry's posts
New browser Chrome from Google)
I've just installed the new Java 6u10RC (1.6.0_10-rc)
It's difficult to say, but it does seem to load faster (before the applet) and
shows less dead times in between loading Java logo and Jmol loading
Hello Avehna
Actually the way I am doing this is not right because both checkboxes are not
synchronized
(when I check box1 the jmol command running on box 2 just disappears )
Can you explain this more? Do you mean that script nr. 2 is interrupted if you
click on Box
1, or that script 2
Yes, I can confirm it's working.
I don't know when I last updated my Chrome browser (it may be updating
itself automatically), but it is at version 0.2.149.30, and Jmol works.
¡Bravo! :-D
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Hi Volker
On 21 Sep 2008 at 13:56, Volker Blum wrote:
1) (minor) For two initially unconnected atoms,
I cannot help much with this.
From
http://chemapps.stolaf.edu/jmol/docs/#connect
it seems that you might need to specify opaque or ModifyOrCreate options
for this to
work.
2) Regarding
On 21 Sep 2008 at 15:50, Volker Blum wrote:
- the sequence of commands
structure HELIX (atomno=17,18,19,27,28,29,37,38,39,47,48,49);
ribbon on
does nothing at all in my case (those are the numbers of the
backbone ...-CCN-CCN-...'s . The whole thing is clearly helical - what am I
Tom, have you tried
echo @variable
?
That works for me in a simple test. But I'm not proficient with the use of
braces.
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Rob, you must take with caution that diagnostics. Browsercheck is rather old*
and its report
is based on the browser identity (userAgent), not by testing the features.
Do you mean that Firefox 2 was working correctly and Firefox 3 fails, on the
same MacOS?
If so, it's probably not that reason
Rob, the file.model is numeric.
So, if you do
load f1.pdb
load append f2.pdb
(or the same,
load files f1.pdb f2.pdb
)
then you need
set backgroundModel 1.1
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Hi Jon
select none should work; being in a button is meaningless. Unless there
has been an error and the script has being terminated. Check the console
or the Java console for errors.
Yes! geosurface does not accept the surface id. Check the doc.
Anyway, you have an easier solution that
Glad the solution suited you, Jon
The general way of finding problems with scripted buttons and such is to
copy the script and paste it one command at a time in the console.
There you easily see if the command works and any errors that show up.
One can draw a line using
draw myID {point} {point}
and, if I want more than 3 nodes, one can draw a smoothed curve:
draw myID curve {point} {point} {point}
However, I find no way to draw a polyline with straight segments as a single
object, since if I do
draw myID
On 25 Sep 2008 at 11:09, rob yang wrote:
That works, although I needed to sleep for 500 instead of 100. the
loadLigands() function is fired
up by body onload=loadLigands();. I am wondering if it's a case of safari
browser does
something different in executing the body onload=...
Thanks, Tom, I know I can do it like that, but I'd like a single object.
I was just wondering how this can be done as curved polyline and not as a
straight polyline.
Bob, maybe could this be implemented?
draw myID line {point} {point} {point}
Bob,
I downloaded it and played in BSPlayer without trouble (WinXP).
Resolution is very good, even when resized.
QuickTimePlayer requested an extra codec and took me to Xvid webpage (a 628
kB download, GNU GPL). After installing, QT does not ask for anything but
shows only a black movie. Maybe
I'll need a state to work with. Is it possible you have 4 files? I don't
think it's cloning itself. I think
there are really four objects all being displayed at the same place and you
are just picking up the
top one and moving it, so it LOOKS like it's being replicated.
You are probably
On 9 Oct 2008 at 10:20, Egon Willighagen wrote:
SourceForge, Inc.
650 Castro Street
Suite 450
Mountain View, CA 94041
USA
Not?
Good point!
Willighagen, Egon and Howard, Miguel. Fast and Scriptable Molecular
Graphics in Web Browsers without Java3D. Available from Nature
Precedings
On 9 Oct 2008 at 9:01, Rzepa, Henry wrote:
It would be interesting to identify all the STM journals that deploy it in
some manner or other.
Sorry, what is STM?
May I remind all of you that there is a place to list any journal you may know
that uses Jmol:
I can confirm that this version fixes the problem with worng element
identification I reported previously.
Thanks, Bob
On 9 Oct 2008 at 11:30, Robert Hanson wrote:
Jmol 11.7.2 now reads the AMBER_ATOM_TYPE line in topology files and
incorporates that as
the type of the atom, which can be
A working demo of this new feature is available at
http://biomodel.uah.es/Jmol/amber/
This uses today's latest 11.7.2dev version of Jmol.
The Amber files sum up to 1.5 MB. I hope they run reasonably fast across the
ocean.
Thanks are due to Dr. Jesús Mendieta (from CBM in Madrid) for providing
Hi Eric
You maybe get some use out of this page of mine:
http://biomodel.uah.es/Jmol/getProperty/
It's an old Jmol version, but things should be the same or similar
The hand-picked atom is marked as selected, so you should be able to get
the info obtained in the page by using any selection
On 2 Nov 2008 at 15:50, Chris Pudney wrote:
Is there any way to provide a hint to the applet that the data is of a
particular format?
Hi Chris
In the load command, there is indeed:
http://chemapps.stolaf.edu/jmol/docs/#load
says:
this resolution process can be overridden by
David,
connect 1.8 {H andetc.
is not correct; you need _H or hydrogen, not H
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On 7 Nov 2008 at 15:59, Richard Steane wrote:
What version of Jmol would this script/command work with?
connect 1.8 {_H and connected(_O or _N)} {_O or _N} HBONDS CREATE
Not sure of the exact boundary, but I'd say any moderately recent.
However, I am still not familiar with the cruly
Sorry, I stand corrected
I mess up my test: both parentheses and braces work the same
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David, have you measured the length of the Hbonds you want to show up?
You might nedd some longer spec.
I've just tested
connect 1.8 {_H and connected(_O or _N)} {_O or _N} HBONDS CREATE;
with
http://doolittle.ibls.gla.ac.uk/top500H/1osaH.pdb
and Jmol 11.6.3 and it creates and draws 12 new Hbonds
Hi Jaime
Have you checked
http://wiki.jmol.org:81/index.php/File_formats#Open_DX
?
There is some info and 3 links there
I've done some test, and this looks like a bug.
My DX file loads Ok in 11.2.14, 11.4.6, 11.5.6, but not in 11.6.4
After
load lisozima.pdb;
isosurface
On 10 Nov 2008 at 15:42, Robert Hanson wrote:
I'll need a sample file
The dx is 11 MB. I've packed it together with the original pdb file in
http://biomodel.uah.es/angel/lisozima.zip
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So I've added a link to the Sourceforge copy of the Scripting Doc in the
main Wiki page, under the Documentation section (lower right box).
If anyone wants to add other mirrors, the page to edit is
http://wiki.jmol.org/index.php/Template:Jmol_Documentation
On 29 Nov 2008 at 8:12, Rzepa, Henry wrote:
http://www.ch.ic.ac.uk/wiki2/index.php/Mod:jmol
I currently have it down to a silly mistake somewhere, probably a
variable in LocalSettings.php. The correct source code is being
generated, including the Jmolinitialize script etc, but it just
Henry, I'm glad that you found the cure for your problem, and to have been a
catalyst in that
cure :)
On 29 Nov 2008 at 14:53, Rzepa, Henry wrote:
In the distribution
http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol-extensions/wiki/MediaWiki/
edit the file Jmol.php to make the
On 30 Nov 2008 at 9:48, Brian Salter-Duke wrote:
That is great news. Thanks, Henry. My page on the Jmol wiki is now
working and I have something I can point the wikipedia tech folks to so
that they can look at Jmol.
Brian, I'm quite surprised that your page has started to work NOW. Unless
Philip Bays wrote:
As I recall, Alchemy was a program for the Mac back in the early 90's
that Tripos sold. I thought it had gone out of existence. Is it
still available, or has it been reborn?
Oh, that may be why I can't find hardly any info on this format.
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