You're right, Rolf, it works for most of the proteins I've tested now, but
fails
for a few. I will have to investigate what is the key.
Thanks for looking at it.
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Thanks to all who have sent suggestions for my talk.
It's great to have such help!
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Defy all challenges. Microsoft(R) Visual Studio 2008.
So I've tried the new minimization, but had hit a stone wall.
I downloaded 11.5.21 from SF (BTW, the popup says 2008-03-02)
Loaded a flat thyroxine molecule in CML format, and issued
$ minimizationSteps = 80
Script completed
$ minimizationRefresh = true
Script completed
$ minimizationCriterion =
Wonderful, Bob!
The newest applet is working very well.
Something funny but very sound:
go to
http://biomodel/Jmol/minimize/minimize.htm
Load the 2D caffeine, then click minimize several times until it stabilizes;
note the sp3 nitrogens
Now click on recalculate aromaticity and repeat several
Hi, I'm trying to use jmolLoadInline()
It works well in Firefox and Opera, but in IE 6 and IE7 I get this error:
Runtime error
line: 377
Error: java.Lang.Exception: java.Lang.Exception: loadInlineString{0} :method
does not exist
The applet and Jmol.js are latest from Bob's site (11.5.22dev)
So I've being playing for a few days with the minimization of structures in
Jmol, and I'm very
happy with the result; I think it will make an excellent educational tool. I'm
feeding Jmol with
2D structures drawn and then exported into MOL format.
(All this runs within a single web page,
Thanks for your comments, Park
On 6 Apr 2008 at 14:30, Park Won-Kyu wrote:
I think the combination of the JME + Jmol is the possible one.
Yes, and also JChemPaint + Jmol (which is what I'm working with; both Open
Source
applets).
and the PR #1830352 implement *moving atom* with ALT + mouse
For MOLfiles witout content in the first line (mine is generated as inline
model by reading a
textarea), the call to
jmolGetPropertyAsString(stateInfo)
returns a string that has
data model inline
followed by a line break and the second line of the MOLfile. It seems that
this is
Sorry if that wasn't clear enough.
I'm reading the state from the original window using
var x = jmolGetPropertyAsString(stateInfo)
and then applying it to the new window using
script javascript:x
On 8 Apr 2008 at 21:56, Angel Herráez wrote:
For MOLfiles witout content
According to a previous report of mine (which went into doc. in the Wiki)
http://www.mail-archive.com/[EMAIL PROTECTED]/msg09232.html
in MOL format files, bond type 8 (described as any) used to be interpreted by
Jmol as
partial bond. Now I see it is not so; bond is not drawn.
I'd like to know
Jmol 11.5.47
Not sure if this is significant, but I'm seeing a strange report in the console
when I make a
distance measurement using the mouse: rather than two atoms, three are reported
Example:
[GLY]79.O #374 16.525 32.072998 40.378998
[SER]83.OG #399 17.914999 35.779 37.742
A recent post of Bob's in jmol-users has prompted me to change the
rotation button and some other icons in the application toolbar.
Can anyone advise if the proper place to put updates is
trunk/Jmol/src/org/openscience/jmol/images/
?
Thanks
Bob Hanson wrote:
Great! Angel, can we have three measurement icons, please -- Distance,
Angle, and Torsion?
Mmmm.
I have several versions of a ruler and a compass, but they don't look great at
20px, so I'm
sticking to the old ruler, which is clearer.
For the angle, I can think of
I was thinking of just a ruler with the letter D, A or T
That's easy enough, but we will have a localizaation problem. Those initials
will mean nothing in some languages.
I'll see what can be done in the graphic arena
-
Thanks for the answers and hints, Nico
4. The animation controls in Atom Chooser, are meant to mean the same as
those in the
toolbar, or should I leave them as they are now? Not sure if that's frame
animation too.
I think they are probably meant to be the same as the application,
Is there a reason for having Close and Exit entries in the application File
menu? Now I
have two nice icons for them, a red X and an onOff red sign (vertical bar
inside an open
circle).
Some time ago I remember discussing that both closed all Jmol windows, while I
expected
Close to close
I vote for a single Exit, Quit or Close. However, we should
probably have a separate Close Window function. In most
applications, Exit and Quit shutdown the application. Close is
used less consistently.
This gives me an idea:
Close this window
Close all windows
A bit long,
Hey, it's solved for me now.
In my case it didn't look like Jonathan's commit was the cause, as the
errors were unrelated. I also tried to go back to a former revision without
any difference. I had already cleared the build folder -several times- and it
din't help.
Now I deleted the whole
Hi all
1)
While pursuing a term that resisted proper translation (localization) in the
pop-up
menu, I've realized that there are about 60 GT terms duplicated in applet.PO
and
app.PO files.
The applet uses only GT terms from the applet.PO file.
The app uses the GT terms in the applet.PO file
The new top menu in the applet console has a Help entry which is not
localized.
Can this be done?
I find a couple of Help entries in
src/org/jmol/applet/Console.java
only one of them is properly capitalized as it appears in the menu, but it
hasn't got the key accelerator H marked as such,
so
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 Java console is
couldn't find file: pop_in_template
I think this has something to do with the recent changes to make this
The fixes are working great. I'm getting fully-Spanish Export to Web
dialogs, help pages and template-based web pages.
But for it to be perfect, we need also the JmolPopIn.js to be localized
(JmolPopIn_xx.js), since it holds an important message, i.e. telling the user
to click in order to get
On 27 Aug 2008 at 16:34, Jonathan Gutow wrote:
While
looking into this I found some other messages that end up in the
generated pages that should be translated.
I haven't seen any more. It may be those which I have already worked on. I
haven't
commited them yet since I wanted to check
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._
(...) 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
On 27 Aug 2008 at 12:25, Nicolas Vervelle wrote:
Hi Angel,
Do you have a list of duplicated terms ?
Maybe it can be modified directly in the code to have them in the correct
classes.
I have one (attached), but I should revise it as I didi it quickly and may have
ommited some.
Plus,
Nico,
this is the list of GT terms duplicated in Jmol.pot and JmolApplet.pot
There are les terms now due to recent addition of accelerators to most
entries; maybe it's not worth the effort.
Let me know if I can help somehow.
About Jmol
{0} Ã...
Atoms
Axes
Bonds
Help
Hetero
History
Jmol Script
On 29 Aug 2008 at 12:14, Jonathan Gutow wrote:
Angel,
Are you sure that it is not using already compressed files? We try
to just copy files we've already processed. Try again starting from
scratch with a new file and let me know. It looks like it works for me.
You're right, I
On 29 Aug 2008 at 14:48, Jonathan Gutow wrote:
It shows up in the page creation data at the bottom. Here's the
mangled text at the end of a document (I've put around parts that
come out funny):
Armaz-n de la pgina y JavaScript generados por la funci-n
exportar a pgina web de Jmol
On 29 Aug 2008 at 15:20, 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.
In case you find a way to flag
Maybe if the html templates are set to charset=utf-8 instead of iso-8859-1
in the meta tag and ?xml tag?
(The PO files are coded in UTF8)
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Build
1)
I use poEdit (Win) for translations --but we have to consider the new,
alternative, web-based
system on --. The PO files have an UTF8 coding, so it's not correct that I use
iso-8859-1as
Bob pointed out. I write directly the accented characters by keyboard and
poEdit codes them
as UTF8 (when
On 30 Aug 2008 at 9:49, Jonathan Gutow wrote:
You can look for yourself. By any chance does the Old
file look ok on your machine, which I assume defaults to Spanish?
Right. WinXP Spanish
The
files are:
Old (didn't work):
On 30 Aug 2008 at 10:26, Robert Hanson wrote:
span /span
might. If that is in the GT expression, then the translator will see that
and, presumably, know to
use this mechanism. It isn't great, because it is nonstandard, but it seems
the only alternative.
Don't know yet what to vote
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 **generating** the page in the Mac may be the key.
I've just generated a page using an app with the old translation (that has
I've commited another GT.escapeHTML() call, on the skeleton sentence at the
footer --
the one that started all this--
I changed every string in my local copy of es.PO file back to accents and
tested. Everything
working here OK --well, nearly, but I will leave that for later on; accents
are a
Jonathan wrote:
special characters in the file names. This does not work when the
script processing engine is used to load and queue a script through
commands like script Herr#0255ez.spt (used by jmolButton).
I did a quick test yesterday and everything worked except the background
Jonathan,
It looks OK.
I will do a more thorough test this evening.
On 31 Aug 2008 at 20:16, Jonathan Gutow wrote:
I think I have got everything working correctly with the special
characters and webexport.
The changes were committed to 11.6.RC13_dev (commit 9844).
Angel, could you please
I
make them look aromatic?
(maybe with the aromatic command? or was it calculate? I never catched
it)
On 17 Jul 2008 at 0:25, Bob Hanson wrote:
I'll need some specific file examples, please.
Angel Herráez wrote:
According to a previous report of mine (which went into doc. in the Wiki
Translated Export to Web is working well, and all special characters in files
are correctly replaced.
As far as I can see, we have Spanish and Brazilian Portuguese completely
translated for this.
Haven't had the chance to test in a Mac yet.
On 31 Aug 2008 at 20:16, Jonathan Gutow wrote:
I
http://jmol.sourceforge.net/download/
needs updating. Current version
I'll take care of updating the website source files side, while Nico finds out
the updating procedure.
I'll also update the Jmol files themselves for the front page and the demo
pages
Great work! Congratulations!
I have commited the update to display 11.6 as current version nr. in the
front page and the update of the applet files for the website.
I want to check that the examples/demos work well, but I cannot do that
right now locally due to the applet path, so I'll test them once the changes
are in the
A few comments/ideas raised by Henry's post:
I also suspect that there must be a very wide spread of versions in that
embedding, possibly going back to Jmol 10 and even earlier. My experience is
that Jmol has excellent backward compatibility, and that there is a high
probability that the
In revision 10022, dleidert has changed the tags for languages (used in the
pop-up menu)
I also think this sounds better this way, but there is a side effect: as far as
I
can see, Jmol orders the entries in the language menu alphabetically.
With the new tags, both English variants will likely
I've done a local build from revision 10030
and the unsigned applet seems to work OK; opens in Spanish, changes languages
from the
popup menu withou a hitch (I'd even say that quicker than before). I tried
English, French,
Portuguese, back to Spanish.
However, the app gets hung at the
On 11 Oct 2008 at 13:14, Nicolas Vervelle wrote:
Really strange : I got security exceptions on the first attempt to view
pages, but now it seems ok.
I've had no trouble.
I'm checking the demo pages and while testing them locally I had some trouble
convincing
the browser to use the new applet
I'd say feature, if it was controllable :-)
This sounds like something I had about a week ago: I was playing a 1-hour video
in
RealPlayer and wanted to capture a still image. So, I paused the player and hit
PrtScr. I
went to my usual image editor, pasted, and the size of the image was
On 3 Nov 2008 at 7:15, Robert Hanson wrote:
You need to start the model with |
If this is not in the wiki documentation, we need to get that there.
I see nothing about loadinline in the Wiki. Any ideas where we have it?
There is something in the website,
If we decide to go for that, a restore option would be nice to the user; it
would run
load
* Edit
** Calculate Hbonds
** Calculate secondary structure
** Calculate aromatic
** Minimize
** Restore original structure
The other editing tools I thought of are invertSelected,
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 seing that the JmolMediaWiki extension inserts it in the
HEAD, and it seems to work.
Anyone has an idea if the location is
On 8 Dec 2008 at 11:24, Robert Hanson wrote:
location is not important. It just sets values.
Thanks, Bob. So I will remove that piece of info from the Javascript Library
documentation.
While playing with the JmolMediaWiki Extension I have, though, found a
situation where the
location is
Nico, I have committed changes in the Jmol MediaWiki Extension (a list of
achievements is
at the end of this post).
Can you please udate the Jmol Wiki?
We don't have a numering system for versions of the Extension, do we? Maybe the
date or
the SVN revision nr. is enough.
* Maybe it's time to
While testing the Mediawiki extension, I am having a
too much recursion error in the Javascript console of Firefox.
I haven't yet been able to track it down to a single page or setup.
The error points to the previousOnloadHandler(); line 1096 in Jmol.js:
function _jmolOnloadResetForms() {
Robert Hanson wrote:
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
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, Nico
The funny thing is that as I was trying to analyze the fix, I was reading the
function as if everything was inside the conditional, then I realized the
braces
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
show menu
Then I saved the text as Jmol.mnu; I also made a copy and edited to my taste,
saving as
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!
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After the latest post by Marko, I have found another little glitch with pop-up
menu Save:
This happens in 11.6.13, not in 11.7.21,
and only from the popup, not from the console (since here the filename is given
explicitly)
and it affects only VRML, POV-Ray, Maya; not the other export formats.
On 17 Jan 2009 at 14:17, Robert Hanson wrote:
In addition, I've added to the VRML
exporter code that stores the atom's actual XYZ and screen XYZ
positions just prior to displaying a label. Angel, you might be able
to use that information to do what you need to do.
Thanks, Bob, that works very
All this playing with the VRML export is making me think.
First we had the POV-ray export, but that's basically a sophisticated image,
right?
Then we have VRML, which I am extending with not much difficulty, thanks to
Bob's
implementation of new bits of code.
I've also prepared X3D export.
On 19 Jan 2009 at 9:44, Robert Hanson wrote:
[...]
The distortion is due to the perspective having the camera too close
to the model.
Are you sure of that difference? See
http://biomodel.uah.es/Jmol/vrml/comparison1.png
I see them much the same.
On 19 Jan 2009 at 9:44, Robert Hanson wrote:
There must be some way of defining the VRML view -- look for a
definition of a 4x4 transformation matrix (includes zoom and
centering) or a 3x3 rotation matrix. Those are available via Viewer
methods.
Don't know what to do with the orientation
Hello Jairav
The model is meant to be roughly representative, so I just want to
draw a ribbon (or rather noodle view where each DNA base is displayed by an
atom (to
simplify)
Yes. It should work if you set the atoms as phosphorus. I think that Jmol will
join them
automatically in
I can confirm John's observation, using a different 2D mol file.
load myMol.mol works
load myMol.zip give extra bonds (between close atoms)
This seems to be due to Jmol autobonding being applied in zipped files. If I
issue
set autobond off
before loading the zip file, then it renders
On 6 Apr 2009 at 13:40, Jairav Desai wrote:
I just want to confirm, so if I use the pdb format, I don't need to specify
these xyz coordinates? i
can just specify the bonds?
No. You need xyz coordinates always; there is no way the atoms can be
positioned without coordinates.
And pdb
I think it happens for 2D mol files that have funny bond distances. If the file
is 3D (and so has proper bond lengths) or it is 2D with reasonable bond
lengths, no problem. But when the file is 2D and has too short bond lengths
(some programs do this, considering that a 2D structural formula
(Apologies if you receive duplicated posts; my email server has gone nuts
last week)
Jairav, I've had a couple ideas:
1. You can generate the necessary xyz coordinates by script
2. Using Jmol connect and then minimize commands can produce the wanted
approach of certain residues
Have a look
Jairav, I've had a couple ideas:
1. You can generate the necessary xyz coordinates by script
2. Using Jmol connect and then minimize commands can produce the wanted
approach of certain residues
Have a look at this:
http://www31.websamba.com/jpeg62/Jmol/gene_simulation.htm
I have used alpha
The doc
http://chemapps.stolaf.edu/jmol/docs/#text14
says that atoms have a settable property atomName.
In 11.7.32, I can set that property (and display it using label
%a), but cannot read it using print or put it into a variable. It
says
script ERROR: unrecognised atom property: atomName
I've noticed that on
http://chemapps.stolaf.edu/jmol/docs/examples-11/carbo.htm
the pop-up minimize does nothing, and also from the console. Is that for
this page or is it broken in 11.7.33_dev?
The Java console says
Interface.java Error creating instance for org.jmol.minimize.Minimizer:
The use of DATA to provide a model inline in a script deletes the
existing model. I was wandering if there is a way to add atoms to the
current model.
I have found that I can do DATA first, then LOAD APPEND (with or
without set appendNew), but not the other way round.
Maybe data append could be
On 23 Apr 2009 at 11:53, Robert Hanson wrote:
That should work already -- I guess it's not documented. It's
data append
Aha! I tried
data append model example
and the parser complained of too many arguments
Thanks!
Mmmm... it's not working well.
I load a model, with 37 atoms. The
On 23 Apr 2009 at 15:57, Robert Hanson wrote:
check model 2
Oh, right. The problem was that the pop-up menu says only one model, and
the frame forward/back buttons in the app toolbar don't work either. After I
typed frame 2 in the console, now the menu says 2 models
But the back menu in the
On 15 May 2009 at 21:19, Aidar Mahmutov wrote:
Now, I'm just interesed in groups. For what reason it exists?
A group is a group of atoms with a common group ID. They have a meaning in
proteins
and nucleic acids, where they are residues (amino acids and nucleotides,
respectively).
In addition,
Egon, thanks for buying the first one.
But you'll have to wait until I write the new one (not sure when)
;-)
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looking to deploy the next
Jonathan, that sounds OK (but I haven't checked in detail, and it's
Java, isn't it? - then I have nothing to say about precise code)
I'd say that the 2 functions could be fused into one. Say if no
insertpt is given, append the string at the end.
http://chemapps.stolaf.edu/jmol/docs/misc/1crn.vrml (1.6 Mb)
Hey, ribbons! and gradient coloring! That's wonderful, Bob
These files are huge -- I wish there were a faster, better way of delivering
3D molecular graphics
over the web... ;)
Yes, that would be great ;-D;-D
I did some
Bob, can I grab the new app for testing? The current Jmol-11.zip at
your site is corrupted (and too small).
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El 29 Jun 2009 a las 10:45, Riccardo Sabatini escribió:
Hi,
i'm a PhD student from italy and i'm writing a modelling
application for nano-structures that will be used as an editing tools
for a DFT code developed
Hello Vikash, and welcome to Jmol
JmolApplet0.jar is not enough. When you use the Jmol.js method (recommended) as
you
are doing, you need all the files that start with JmolApplet0
(And you don't need JmolApplet.jar , which is just an alternative way to use
the applet)
You don't need the jmol
The new buttons in the console/script editor are not internationalized (they
don't appear in the .PO file): Editor, Check, Step .
Top (meaning Go to top, I guess) should be made different to the existing
one (meaning View from top)
I see the terms are in ScriptEditor.java, but for some reason
Hi Bob
I've been struggling with testing the draw arc until I've found there is a
typo in the
doc (I recall discussing this before, but cannt find a trace in the email
archives)
http://www.stolaf.edu/academics/chemapps/jmol/docs/#draw
says:
ARC {pt1} {pt2} {ptRef} {theta, nDegreesOffset,
Hello Riccardo
Is there a chance that the newline characters are not being
recognized or correctly parsed? Inline models often suffers from the
different newline standards across Operatign Systems.
If I remember correctly, you may use the | character to indicate
new lines if needed (search the
Bob, can you supervise my last commit? Thanks
I read about compacting VRML files, one trick is to reduce precision in
numbers, i.e. write
less decimals. I've chosen 3, which applies to xyz coords, cylinder lengths,
and colors.
I'm not sure if the same should be done for POV-Ray (I don't know
On 18 Jul 2009 at 9:12, Robert Hanson wrote:
Molecule name -- I see -- as part of the header comments, right?
Right
viewer.getModelSetName()
that can come back null.
Oh yes, I found out yesterday after several blind trials. At first I was trying
Viewer.getModelSetName() --following the
Bob wrote (on jmol-users):
also put on your list getting the perspective right. Does the VRML use a 4x4
matrix to
define the orientation, by chance?
I assume you mean the user's point of view fo the model.
There is a viewpoint orientation in vrml that takes 4 values. I imagine that
could be
Bob, the new orientation in vrml is giving me trouble; if I rotate the model
before export, in
the vrml the model is often out of sight. Sometimes it comes into view by
rotating around in
the vrml viewer, other times it's hard to catch it.
It may be correctly reproducing the orientation in
Hi all
Following Bob's big improvement on VRML export, I have picked up an old project
and
updated the (unreleased until now) exporter for X3D format.
X3D is an XML version of VRML, so features are similar and having it is no
great fuss. I just
felt like doing it.
I've tested it quite a bit
Bob,
Things have certainly improved in the orientation+camera of the vrml exporrt.
However, I
wasn't too happy yet ;-). I am testing with 2 models, alanine and lysozyme, and
the latter is
still far away (zoomed out) with respect to Jmol view.
So I've tested different approaches, less
Welcome back, Nico
Hope you had nice relaxing holidays in the beach.
Yes, I recently saw (doing a local build) that the problem was that
the POT file had not been rebuilt. So it will work well now.
BTW,
Top and Top could be a problem.
seems not to be, because the item in the menubar has Top
Sorry, it seems I forgot to mention...
I'm speaking of the application. Load from PDB is active, Load full unitcell is
active, the
Save entries are active.
On 21 Jul 2009 at 15:11, Robert Hanson wrote:
because it's not the signed applet.
That's darned good, Bob. Great job!
The X3D export is now up-to-date with that.
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Hi Yael and Ira
Diificult to say from here, but you should be able to draw the planes you want
using either 3
points or 3 atoms as the coordinates defining the plane orientation. You can't
feed the
angles, but you can calculate the coordinates from the angles and pass them to
Jmol, can't
The full spec of the draw command is on the Jmol Scripting Documentation
webpage.
Regarding combination of several parameters, you will have to experiment.
May I suggest that this kind of questions is adequate for jmol-users, not
jmol-developers
Bob, this sounds very interesting. I'm quite keen on joining you.
The dates seems fit for my plans. I'll research a bit more into the symposium
details and
how/if I can make profit of the trip (i.e get funding, maybe present a
communication). It
would be great to meet you in person and share
Hi, Tzontonel
Here they are:
http://www.stolaf.edu/academics/chemapps/jmol/docs/index.htm#moveto
moveto timeSeconds FRONT|BACK|LEFT|RIGHT|TOP|BOTTOM
for example: moveto 1 back
- reset value
Yes, that is reset
- and when structure move... show boundbox on (is not necessary if you don't
Hi all
I am a bit confused:
there are two kinds of instances of the Top token: one in the popup menu,
View, meaning
view from top, another in the script console and script editor, meaning go
to top.
On the localized result in Spanish, I am seeing funny things.
The JmolApplet-es.po file has a
Thanks, Nico
And we also have a special situation with our 2 .pot files : if the same
sentence is in the 2 .pot
files, only one translation will be used in the application (because the Java
code can't decide
which one to use and looks for the first available translation).
Aha, so my
On 30 Aug 2009 at 18:12, Nicolas Vervelle wrote:
Hi Angel,
This is a general problem when an English word can be translated differently
depending on the
context, since the English word is the key used for finding the translation.
Basically, this happens
because you can only create
Hello Robert
Thanks for reporting this.
I knew that the model's internal name was being used for the exported
filename, but none of us thought that would be a problem, as you have
now found. The error due to special characters will certainly have to
be taken care of; I'll see what I can do,
OK, I think I have it pinned down.
Right now, the POV-Ray exporter invokes a file save dialog, while the other
exporters don't.
I can see no reason for this difference. (The POV-Ray export is a bit different
because it
must generate 2 files, but as far as I can see the code for that is
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