Original Message
Subject: Re: [Jmol-developers] [sage-devel] Re: Jmol and
MathematicsVisualization
Date: Tue, 25 Dec 2007 20:07:25 -0700
From: William Stein [EMAIL PROTECTED]
To: [EMAIL PROTECTED], jmol-developers@lists.sourceforge.net
fixed for RC11 -- thanks for spotting that Angel.
On Wed, Aug 27, 2008 at 9:24 AM, Angel Herráez [EMAIL PROTECTED] wrote:
On 11.6.RC10, the Export to Web module fails to save the template files.
On the saved folder, I only have JmolPopIn.js, the PNG file and the SPT
file.
Error in the Jmol
another option is even better, I think. We just set up a set of GT._(...)
terms in Jmol and then bulk-load them into the JavaScript on the fly. In the
JavaScript we simply put in a set of keys, like $MSG1$ that are then
replaced on the fly. The GT system will recognize all these just like any
:
That seems like the answer. I may have some time to look into it
tomorrow. I have a few handouts to get ready for the start of
classes first, but I will see what I can do.
Jonathan
On Aug 27, 2008, at 7:50 PM, Robert Hanson wrote:
another option is even better, I think. We just set up a set of GT
at least in Firefox3 it is important to have that iso-8859-1 there. using
utf-8 creates problems.
Jonathan, I'm not seeing the improper coding that you are seeing.
Bob
On Fri, Aug 29, 2008 at 5:33 PM, Angel Herráez [EMAIL PROTECTED] wrote:
Maybe if the html templates are set to charset=utf-8
On Aug 29, 2008, at 3:20 PM, Robert Hanson wrote:
Jonathan, you might want to go back and flag all GT messages that
would go into HTML in a special way. I think you are right that the
translation of special characters has to be done differently in
that case.
Dr
[EMAIL PROTECTED] wrote:
On Aug 29, 2008, at 9:31 PM, Robert Hanson wrote:
I'm not following what the idea is here. First let's confirm that
it's really an issue. I'm not having the problem. Jonathan is.
Tagging translations in any way is going to be problematic. We have
OK, this one I've not seen before. I must be forgetting something when
building.
Exception in thread QueueThread0 java.lang.AbstractMethodError:
org.jmol.symmetry.Symmetry.setPointGroup(Lorg/jmol/api/SymmetryInterface;[Lorg/jmol/modelset/Atom;Ljava/util/BitSet;ZFF)Lorg/jmol/api/SymmetryInterface;
of all the molecules in that directory that are
xml files. Prototype.js (http://www.prototypejs.org/) is Javascript
framework that makes some AJAX (like XMLHttpRequest and DOM manipulation)
stuff a bit easier.
Dean
On Fri, Aug 29, 2008 at 10:20 PM, Robert Hanson [EMAIL PROTECTED]wrote
OK, so if it is necessary to use
aacute;
then we still have problems with regard to marking. You are saying that any
GT expressions headed toward HTML must be escaped in this HTML-only sort of
way. We are not set up to make such a distinction in the translations.
So, if this really is the
Two pages to check:
http://www.alanwood.net/demos/ent4_frame.html
http://www.fileformat.info/info/unicode/block/latin_supplement/utf8test.htm
question is whether the #; method works for you. If so, let's just go
with that and let translators translate as usual into unicode. I know that's
OK, here's another simple possibility. We simply change those character
codes entered by the translator or user that are going to HTML by converting
them to the hex value:
#x00E1;
for example. That way it's our job, not the translator's or user's job, to
manage this.
Bob
On Sat, Aug 30, 2008
I added the method
GT.escapeHTML(String msg)
Translators do not need to do anything special in translating the HTML now.
If Angel wants, he can use aacute;, although I think but he can just as
well just do as he has been doing for all Jmol translations.
Users can enter the page title in
Sí, está perfecto. Muy interesante. Es posible.
On Sat, Aug 30, 2008 at 12:26 PM, Angel Herráez [EMAIL PROTECTED]wrote:
On 30 Aug 2008 at 11:52, Jonathan Gutow wrote:
I get the same result locally on a mac. I haven't tried the files
locally on Linux or Windows.
Aha!
I think that
Just added a couple more GT.escapeHTML() calls. Around the names of the
buttons and such.
On Sat, Aug 30, 2008 at 12:16 PM, Robert Hanson [EMAIL PROTECTED] wrote:
I added the method
GT.escapeHTML(String msg)
Translators do not need to do anything special in translating the HTML now
great to have that resolved. Thanks, Jonathan and Angel.
On Sat, Aug 30, 2008 at 1:20 PM, Jonathan Gutow [EMAIL PROTECTED] wrote:
On Aug 30, 2008, at 12:31 PM, Angel Herráez wrote:
Jonathan, to finish clarifying this, attached is the file set I
just generated. Please add the
applet
characters that are not 0..1a..zA..Z? The only problem I really see
is that this might become an issue in non-western languages.
Jonathan
On Aug 31, 2008, at 9:58 AM, Robert Hanson wrote:
great to have that resolved. Thanks, Jonathan and Angel.
On Sat, Aug 30, 2008 at 1:20 PM, Jonathan
, 2008, at 11:49 AM, Robert Hanson wrote:
we should be saving the scripts as part of the HTML file in !-- --
comments, then loading them from that. The whole .spt business
should go.
In the .js file we need:
function getScript(name) {
var tag = -- JMOL SCRIPT + name
, Robert Hanson [EMAIL PROTECTED]wrote:
OK, that's fixed. It was a problem with my uploading -- My Filezilla
script hadn't been updated to include the additional symmetry class files.
So although JmolApplet.jar worked, JmolApplet0.jar didn't. Same for signed.
Dean, your page is working now -- it's
-- Forwarded message --
From: SourceForge.net Team [EMAIL PROTECTED]
Date: Tue, Sep 2, 2008 at 10:46 PM
Subject: SourceForge.net Subversion service downtime scheduled 2008-09-04
To: [EMAIL PROTECTED]
On 2008-09-04 at 04:00 UTC, Subversion service write operations will be
offline
fellow web developers,
In exploring more the use of JSON in one of my projects, I ran across this
site
http://www.json.org
and particularly this script:
http://www.json.org/json2.js
I encourage everyone who does JavaScript coding to read through this script
and understand what it does, even
Jmol 11.6.RC14 introduces one last touch worthy of a new version marking:
The signed applet now allows writing to a local drive, with user approval.
All actions of the WRITE command that create files are active for the signed
applet, giving a popup dialog for the user to confirm file save, change
that's fixed now. All files are uploaded -- Nico -- time for RC14. Thanks.
Bob
On Thu, Sep 11, 2008 at 2:19 PM, Robert Hanson [EMAIL PROTECTED] wrote:
Jmol 11.6.RC14 introduces one last touch worthy of a new version marking:
The signed applet now allows writing to a local drive, with user
looks fixed to me.
On Thu, Sep 11, 2008 at 6:52 AM, Miguel [EMAIL PROTECTED] wrote:
Both
http://jmol.org/
http://www.jmol.org/
are broken; they show an Apache info page
wiki.jmol.org is working, though
Looks like a problem with the domain hosting service for jmol.org.
I have
Jmol Developers,
As a preliminary start to releasing Jmol 11.6 next week, I've created a
branch for it. No new features, I promise! Any bugs we find in the next week
(and for the forseeable future) should be entered into BOTH trunk and that
branch.
Next week I will change the version of the
, 2008 at 5:42 AM, Egon Willighagen
[EMAIL PROTECTED] wrote:
On Sat, Sep 27, 2008 at 6:33 PM, Robert Hanson [EMAIL PROTECTED] wrote:
I'm hoping we can release 11.6 Wednesday. Please finish all translations
and
notify me of bugs before then.
Translated applet and app into NL. Quite a few
OK, so it might be worthwhile to check out some more files like this. Rolf,
can you send me some example M-JPEG files that work for you. I'm willing to
give it one more shot.
Bob
On Mon, Sep 29, 2008 at 10:37 AM, Rolf Huehne [EMAIL PROTECTED]wrote:
Robert Hanson wrote:
[switching to jmol
On Fri, Oct 3, 2008 at 4:01 PM, Eduardo Sanz García [EMAIL PROTECTED]wrote:
Hi all,
I was wondering if Jmol could add support to display electron density
maps, for example MRC, that are used in cryoEM.
See:
On Mon, Oct 6, 2008 at 3:19 AM, Nicolas Vervelle [EMAIL PROTECTED]wrote:
On Mon, Oct 6, 2008 at 1:21 AM, Robert Hanson [EMAIL PROTECTED] wrote:
Are translators aware that one need not indicate translations of a
language variant for a country that is already in the primary language
Right now the way it works is that if any language other than en_US is
requested, then all translations are downloaded, because they are all in the
same package. This is the 200K I was referring to. The only solution to that
is to have the different translations in different packages and different
Nico, I've made the 11.6 branch and checked in all my revisions for 11.7.1
as well. So please release both of those.
Fellow developers -- bug fixes now need to be made to BOTH the 11.6 branch
and the 11.7 trunk. New features only for 11.7 trunk.
Thanks.
Bob
--
Robert M. Hanson
Professor of
, Robert Hanson [EMAIL PROTECTED] wrote:
Nico, I've made the 11.6 branch and checked in all my revisions for 11.7.1
as well. So please release both of those.
Fellow developers -- bug fixes now need to be made to BOTH the 11.6 branch
and the 11.7 trunk. New features only for 11.7 trunk.
Thanks
[oops - hit send prematurely]
VERY preliminary support for cryo-electron microscopy imaging. Bugs there,
so not really an announcement of that. Just letting you know that it is
happening.
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
Robert,
What's Sun Wonderland?
Certainly sounds odd. At startup there is very little memory necessary -- If
you don't get a splash screen then something else is wrong. Fully loaded my
memory indicator says only 9.9 Mb are being used for the app after loading.
The application should start much
On Wed, Oct 8, 2008 at 12:26 PM, Nicolas Vervelle [EMAIL PROTECTED]wrote:
On Wed, Oct 8, 2008 at 7:06 PM, Robert Hanson [EMAIL PROTECTED] wrote:
First, under Windows, I have to double the \ for the coordinates file (I
have to use simple \ for the topology file, and double
http://jmol.sourceforge.net/download/
needs updating. Current version
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is
to install ever.
Bob
On Wed, Oct 8, 2008 at 1:40 PM, Nicolas Vervelle [EMAIL PROTECTED]wrote:
On Wed, Oct 8, 2008 at 12:17 AM, Robert Hanson [EMAIL PROTECTED] wrote:
-- translation en_GB
-- commented out in GT.java
-- will be back in as soon as we can get those translations spun off out
Henry, I think there has to be a balance between allowing new features and
preserving the integrity of the initial publication. The nightmare of some
upgrade breaking a published work is disturbing. An author has published
what they published. I'm not sure it would be appropriate to automatically
machine to see if the proper jar files
are being loaded from the server.
Bob
On Thu, Oct 9, 2008 at 7:00 AM, Nicolas Vervelle [EMAIL PROTECTED]wrote:
Hi,
On Wed, Oct 8, 2008 at 11:19 PM, Robert Hanson [EMAIL PROTECTED] wrote:
They have to be in separate packages. Once one class of a package
easy enough. There is an algorithm that just needs to be augmented. If
there's a definitive way of doing this, I'm all ears.
Bob
On Thu, Oct 9, 2008 at 4:57 AM, Angel Herráez [EMAIL PROTECTED] wrote:
I have being able to test successfully some MD files from Amber using
11.7.1 It works very
was there a URL reference for that topology file?
On Thu, Oct 9, 2008 at 8:43 AM, Robert Hanson [EMAIL PROTECTED] wrote:
easy enough. There is an algorithm that just needs to be augmented. If
there's a definitive way of doing this, I'm all ears.
Bob
On Thu, Oct 9, 2008 at 4:57 AM, Angel
Matt, good to hear this! Comments below. - Bob
On Wed, Oct 8, 2008 at 10:09 PM, Matthew Zwier [EMAIL PROTECTED] wrote:
Hi all,
A few days ago, Bob Hanson mentioned that improved support for display
of MD trajectories is on the docket for 11.7. I'm interested in
surveying the lay of the
Actually, the order is just the order in the list in code:
languageList = new Language[] {
new Language(ca,GT._(Catalan), true),
new Language(cs,GT._(Czech),true),
new Language(da,GT._(Danish), false),
Hey, Matt, you might be in luck.
On Thu, Oct 9, 2008 at 2:01 PM, Matthew Zwier [EMAIL PROTECTED] wrote:
At least, I think you can Supposed to be able to. You are just
limited
to one trajectory step from EACH sequence loaded. I can't imagine why
that
would take any major amount of
I've checked in a bit of code that checks first to see if the appropriate
language jar file exists and is readable before trying to load it as a
class. I think that requires two downloads -- one for the check and one for
the class definition, but it's still probably worth it. Nico, if you can see
Ah, missed this message. Maybe that's all there is to it. OK. We do check to
see that we are only loading languages that are on the list. So maybe this
is all we need.
On Thu, Oct 9, 2008 at 11:52 PM, Nicolas Vervelle [EMAIL PROTECTED]wrote:
On Fri, Oct 10, 2008 at 1:00 AM, Robert Hanson
/new.htm?topic=1
JAR files for 11.7.3 are in
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
Bob
On Thu, Oct 9, 2008 at 10:09 PM, Robert Hanson [EMAIL PROTECTED] wrote:
Hey, Matt, you might be in luck.
On Thu, Oct 9, 2008 at 2:01 PM, Matthew Zwier [EMAIL PROTECTED] wrote
The -c flag checks scripts, but it also does all the file opening, and that
will take time. To check a script without file loading, you need to create a
little script that contains:
script xxx.spt check noload
and then use
Jmol -s thatscript.spt
Bob
On Sat, Oct 11, 2008 at 4:44 PM, Robert
I don't think so. I'll check. I usually do the script running, not just
checking, so we'll see.
On Sat, Oct 11, 2008 at 4:22 PM, Nicolas Vervelle [EMAIL PROTECTED]wrote:
Hi,
Script checking seems very slow with the latest versions (as if it was not
only checking the script, but also running
Jmol Developers,
I finally got around to adding Andy Turner's Gaussian Input dialog -- it's
very nice. It's under File...Export
Checked in as part of 11.7.3
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
Jmol Developers,
I finally got around to adding Andy Turner's Gaussian Input dialog -- it's
very nice.
It's under File...Export
Checked in as part of 11.7.3
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
argument there ?
Nico
On Sat, Oct 11, 2008 at 11:58 PM, Robert Hanson [EMAIL PROTECTED]wrote:
The -c flag checks scripts, but it also does all the file opening, and
that will take time. To check a script without file loading, you need to
create a little script that contains:
script
I think what has changed is that it is now opening the files remotely -- the
default directory is being set to
defaultdirectory=http://chemapps.stolaf.edu/jmol/docs/examples-11/data;
That's so that the files are found.
Bob
On Sun, Oct 12, 2008 at 8:39 PM, Robert Hanson [EMAIL PROTECTED] wrote
OK, Nico. I get it. I had messed up the -c and -C flags. I've uploaded
corrections as part of 11.7.4_dev. MonsterScript checks rapidly.
Bob
On Sun, Oct 12, 2008 at 8:41 PM, Robert Hanson [EMAIL PROTECTED] wrote:
I think what has changed is that it is now opening the files remotely
Matt, you are SO in luck.
1) You can define the array data, but it seems to me more appropriate just
to define a starting point for each. Right? Something like this should do
the job:
# Jmol math here
function runAnimation()
frame *
display none
var timeStep = 10 #whatever
var startTimes =
really! Must be a feature ;)
A binary search through old JAR files tracks this down to sometime between
11.3.37 and 11.3.38, October 23, 2007, revisions 8507-8513
On Wed, Oct 15, 2008 at 3:05 PM, Nicolas Vervelle [EMAIL PROTECTED]wrote:
Hi,
I started watching a documentary with VLC on my
make that between 11.3.38 and 11.3.39.
On Wed, Oct 15, 2008 at 4:29 PM, Robert Hanson [EMAIL PROTECTED] wrote:
really! Must be a feature ;)
A binary search through old JAR files tracks this down to sometime between
11.3.37 and 11.3.38, October 23, 2007, revisions 8507-8513
On Wed, Oct 15
ok, I found it. Do you want to keep it or not?
Bob
On Wed, Oct 15, 2008 at 4:35 PM, Robert Hanson [EMAIL PROTECTED] wrote:
make that between 11.3.38 and 11.3.39.
On Wed, Oct 15, 2008 at 4:29 PM, Robert Hanson [EMAIL PROTECTED] wrote:
really! Must be a feature ;)
A binary search
By the way, this doesn't work with RealPlayer -- must be something odd about
VLC Media Player. What do you suppose?
Bob
On Wed, Oct 15, 2008 at 4:48 PM, Robert Hanson [EMAIL PROTECTED] wrote:
ok, I found it. Do you want to keep it or not?
Bob
On Wed, Oct 15, 2008 at 4:35 PM, Robert
OK, this is some bizarre bug in the video system. It turns out that if the
background is set to 0x0001, this odd transparent effect is created. You
can do this with any version of Jmol -- I just effected it with Jmol 10.x.11
(June, 2006).
Prior to Jmol 11.3.39, what you do is use
One LAST observation -- if you uncheck the VLC Media Player's
tools...preferences...Video...Display...[x] Accelerated video output
box, then the effect goes away.
On Wed, Oct 15, 2008 at 11:00 PM, Robert Hanson [EMAIL PROTECTED] wrote:
OK, this is some bizarre bug in the video system. It turns
(after you quit and restart VLC Media Player)
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK win great prizes
Grand prize is a trip
rendering so incredibly fast, and one has to think very carefully before
adjusting them.
Bob
On Wed, Oct 15, 2008 at 7:53 PM, Robert Hanson [EMAIL PROTECTED] wrote:
By the way, this doesn't work with RealPlayer -- must be something odd
about VLC Media Player. What do you suppose?
Bob
It's fairly costly, but for small systems it might not be too bad. You can
certainly test this yourself -- just write a function that changes frames
and does the recalculation rather than just doing the animation. Or set up
an animFrameChange callback that includes autobond
On Mon, Oct 20, 2008
Before doing that, could you please try again with the original code, but
rename the resource
UFF.txt
?
I'd like to know if the problem is that the .prm is sending some odd MIME
type to Url.getContent()
Bob
On Thu, Oct 23, 2008 at 7:44 AM, SourceForge.net [EMAIL PROTECTED]wrote:
Bugs item
(two places that's referred to in ForceFieldUFF.java)
On Thu, Oct 23, 2008 at 8:08 AM, Robert Hanson [EMAIL PROTECTED] wrote:
Before doing that, could you please try again with the original code, but
rename the resource
UFF.txt
?
I'd like to know if the problem is that the .prm
Huehne [EMAIL PROTECTED] wrote:
Robert Hanson wrote:
I'll look into changing that, Rolf, if you feel it to be important. It
was
necessary to have the background distinct from any actually used color,
and
this seemed to be a simple way to do it. At the time I couldn't think of
a
better way
[was Jmol-users]
Li,
An interesting idea, to use the ScriptWindow console in other applications.
It was really designed as a Jmol application-specific class.
The public status of methods in Viewer are specific to how Jmol uses those.
Periodically people ask for classes to be made public, and
Nico, I just finished with 11.7.6.
For the record, here's how I implemented atom typing in Mol2Reader.java:
1) Using the information in
http://www.chem.cmu.edu/courses/09-560/docs/msi/ffbsim/B_AtomTypes.html, I
created a list of all designated force field atom types [1].
2) An atom type in field
) Give up. Return Xx.
Bob
On Thu, Oct 30, 2008 at 1:26 PM, Robert Hanson [EMAIL PROTECTED] wrote:
Nico, I just finished with 11.7.6.
For the record, here's how I implemented atom typing in Mol2Reader.java:
1) Using the information in
http://www.chem.cmu.edu/courses/09-560/docs/msi/ffbsim
You need to start the model with |
If this is not in the wiki documentation, we need to get that there.
param name=loadInline
value=|4 MOPAC-Graphical data Version 2007.7.156W|
80.000 0.000 0.000 -0.4225|
61.2108153 0.000 0.000 0.2364|
... /
just then use something as simple as:
jmolScript(document.body.innerHTML.split(--JMOL EMBED--\n)[1])
and you are done. So if any of that could get in there, that would be good.
Bob
On Mon, Nov 3, 2008 at 2:49 PM, Angel Herráez [EMAIL PROTECTED] wrote:
On 3 Nov 2008 at 7:15, Robert Hanson
oh -- except I forgot you need \n in the JavaScript on each line:
var script = data \model\\n\
@TRIPOSMOLECULE\n\
etc.
On Mon, Nov 3, 2008 at 3:22 PM, Robert Hanson [EMAIL PROTECTED] wrote:
Right -- so the important thing is to say that the first character should
be the delimiter -- it's
On Mon, Nov 10, 2008 at 6:22 AM, Angel Herraez [EMAIL PROTECTED] wrote:
Both app and applet, the topmost entry in the pop-up menu shows the
molecule name, but the first submenu entry says Minimize and indeed
it runs minimization!
Something you don't like about that?
Same in 11.7.11
certainly an idea.
On Mon, Nov 10, 2008 at 8:57 AM, Angel Herraez [EMAIL PROTECTED] wrote:
El 10 Nov 2008 a las 6:24, Robert Hanson escribió:
Something you don't like about that?
Oh, I rather love it!
But don't think it is the most logical place to put it...
I though it was overwriting
The full chemapps documentation site is actually already at SourceForge, but
I don't update that as frequently as my own site. It's under
trunk/jmol-documentation/script_documentation -- but that's a bit old.
Bob
On Wed, Nov 12, 2008 at 12:31 PM, Rolf Huehne [EMAIL PROTECTED]wrote:
Hi
yes -- that's the place. It's fixed. Somehow I had #comment lines going in
without a [0] element.
On Thu, Nov 13, 2008 at 7:23 PM, Jonathan Gutow [EMAIL PROTECTED] wrote:
Ok,
I think I found where the array index goes out of bounds, but I
don't see how. If I'm reading the following
I've checked in all the files I have in all the main interactive script
documentation directories. If there were some way we could do this so that
that's all I have to do, it would be great. I could certainly be more
diligent about it. I didn't upload all the files in examples-11.
--
Robert M.
ok, that's checked in.
Now we need a system to ensure these are synced well. What do you recommend?
On Fri, Nov 14, 2008 at 7:24 AM, Rolf Huehne [EMAIL PROTECTED] wrote:
Robert Hanson wrote:
I've checked in all the files I have in all the main interactive script
documentation directories
wonderful!
On Fri, Nov 14, 2008 at 8:36 AM, Rolf Huehne [EMAIL PROTECTED] wrote:
Robert Hanson wrote:
ok, that's checked in.
Now we need a system to ensure these are synced well. What do you
recommend?
On your side it is very easy. Just check in any changes with 'svn' as
soon
In Debug perspective, Navigator -
click on org.jmol.applet.Jmol.java
(menu) Debug... Java Applet (in left panel) [new] (button at bottom)
parameters tab:
height
width
signed true
Should work.
On Sat, Nov 15, 2008 at 8:35 AM, Jonathan Gutow [EMAIL PROTECTED] wrote:
Dear All:
Jonathan -- you can use
set debugscript true
to follow the statements that are being executed as they execute.
On Sat, Nov 15, 2008 at 6:39 AM, Jonathan Gutow [EMAIL PROTECTED] wrote:
Bob,
I think you fixed some other things when you fixed the crash on goto
problem. The problems
On Mon, Nov 17, 2008 at 12:03 PM, Rolf Huehne [EMAIL PROTECTED]wrote:
Robert Hanson wrote:
wonderful!
I noticed that the date at the bottom of the documentation didn't change
in spite of some changes reported by 'svn update' on the documentation
today.
It would be better if the date would
I've uploaded a new cmds.js and code.js that sets the default to 11.6 and
adds new information about some of the more recent options in Jmol 11.7.
Bob
On Mon, Nov 17, 2008 at 8:13 PM, Robert Hanson [EMAIL PROTECTED] wrote:
That date should change any time I upload cmds.js, which is the main
this is fixed -- in the mean time, just add a space after the minus sign --
Jmol is simply misreading -17.
Bob
On Tue, Nov 18, 2008 at 12:56 PM, SourceForge.net
[EMAIL PROTECTED]wrote:
Bugs item #2309941, was opened at 2008-11-18 17:31
Message generated for change (Comment added) made by
Very interesting to see this in context. Thanks, Egon!
On Wed, Nov 26, 2008 at 6:25 AM, Egon Willighagen
[EMAIL PROTECTED] wrote:
Hi all,
not sure if this analysis was already posted here, in which case I missed it:
Rolf, it is great that you are tackling this.
On Wed, Nov 26, 2008 at 8:02 AM, Rolf Huehne [EMAIL PROTECTED] wrote:
Hi developers,
the increasing power of Jmol is fantastic. But if this power is used
within the applet it greatly enhances the danger of freezing Jmol by an
out of memory
sorry -- pressed SEND prematurely.
Rolf, please check what I just checked in for Jmol 11.7.14. I think it
just might work for you.
-- Out of Memory errors -- Java heap space -- now caught by the
script processor and image creator.
-- jmolGetPropertyAsString(errorMessage) returns the error
an out-of-memory error, I don't know.
Bob
On Wed, Nov 26, 2008 at 1:22 PM, Robert Hanson [EMAIL PROTECTED] wrote:
sorry -- pressed SEND prematurely.
Rolf, please check what I just checked in for Jmol 11.7.14. I think it
just might work for you.
-- Out of Memory errors -- Java heap space -- now
As long as it is not assured that Jmol can work normally afterwards,
freezing might be better (possibly after sending an appropriate error
message).
freezing is never better. I'll look into that error message. I did
make a few changes just this morning. So take a look at that.
Note that it
I need some help from our power Java programmers (Nico, Charles, others).
I'd like us to discuss how do handle out of memory issues. I've tried
just catching these errors, and it works sometimes, but it's not
reliable.
As a starting point, there's an interesting presentation by John
Boyland at
Rolf and others -- I've checked in some refactoring of Viewer,
FileManager, and the adapters as well as some additional code for
handling of OOME conditions. Please check it out.
I had quite a bit of luck, but wasn't 100% successful in surviving OOM
errors with the applet. After several successful
location is not important. It just sets values.
On Sun, Dec 7, 2008 at 10:17 AM, Angel Herráez [EMAIL PROTECTED] wrote:
Documentation
http://jmol.sourceforge.net/jslibrary/index.en.html#jmolInitialize
says that jmolInitialize() should be located in the BODY of the html page.
However, I am
Already there.
When you load the applet, after initialization but before the
jmolApplet command issue:
_jmol.noEval = true
* This allows callbacks but does not allow the script constructs:
*
* script javascript:...
* javascript ...
* x = eval(...)
*
On Tue, Dec 9, 2008 at 11:24
yeah, that sounds right.
_jmol.previousOnloadHandler is being assigned to itself by the
execution of that function twice.
We set up the initialization business so that it would only run once
(I thought). This function is being run multiple times on your page,
perhaps because you have multiple
also -- you could set defaultdir and defaultjar, then just not ever
run jmolInitialize()
On Wed, Dec 10, 2008 at 2:45 PM, Angel Herráez [EMAIL PROTECTED] wrote:
On 10 Dec 2008 at 21:13, Nicolas Vervelle wrote:
try adding { after the test and } at the end.
Yes! That does the trick.
Thanks,
Thanks, Angel. I'll look into that.
On Wed, Jan 7, 2009 at 12:18 PM, Angel Herráez angel.herr...@uah.es wrote:
Hi all
While trying to setup a custom pop-up menu, I have found some problems that
apply even to the default menu
(tested in applet, 11.6.9)
What I did was open the app and type
this is fixed. Problem only in 11.7, not 11.6.
On Thu, Jan 8, 2009 at 6:28 AM, Angel Herraez angel.herr...@uah.es wrote:
This finding was prompted by Marko Reza's recent post to jmol-users
and it looks like a bug.
Tested in 11.7.20 app:
I load a model, then pop-up, Save, State:
ERROR en
oh, good. I'll release that, then.
On Sat, Jan 10, 2009 at 12:30 PM, Angel Herráez angel.herr...@uah.es wrote:
Hi Bob
I've built the 11.7.21_dev applet from SVN 10543 revision, and all my
problems using custom menus have gone away.
Thanks for the efforts!
version=11.6.14_dev
# bug fix: user menu write povray/vrml/maya missing quotation marks in command
On Mon, Jan 12, 2009 at 2:32 PM, Angel Herráez angel.herr...@uah.es wrote:
After the latest post by Marko, I have found another little glitch with
pop-up menu Save:
This happens in 11.6.13,
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