version=12.1.17
# new feature: isosurface ROTATE quaternion
#-- rotates an isosurface based on a quaternion
#-- a display property, like OFFSET or SCALE3D
#-- useful if model coordinates are changed and an isosurface is present
#-- rotations are cumulative.
#-- rotations are
bug fixed. It is a modifier of CALLBACK_LOADSTRUCT that wasn't being sent.
now in JmolConstants (was in Viewer):
public final static int FILE_STATUS_NOT_LOADED = -1;
public final static int FILE_STATUS_ZAPPED = 0;
public final static int FILE_STATUS_MODELSET_CREATED = 3;
public final
On Sat, Nov 6, 2010 at 6:24 AM, Dr. Christoph Gille
christoph.gi...@charite.de wrote:
Hi Bob
It does sound interesting. Clicking on the Jmol logo does get you the
most
recent menu already.
That is a clever idea!
We're talking about the application here, right?
These are the magic
You want
ZAP 1.1
not
DELETE 1.1
ZAP actually removes the model; DELETE just marks atoms as deleted.
On Sun, Nov 7, 2010 at 11:35 AM, Dr. Christoph Gille
christoph.gi...@charite.de wrote:
Though the only molecule is deleted, there are still atoms when using the
API.
Here the details:
1) Make sure you have no references to any Jmol fields or classes (except
Viewer!).
2) Make sure all your event listeners are nulled, as they constitute class
instance references.
3) Issue:
viewer.setModeMouse(JmolConstants.MOUSE_NONE)
viewer = null
On Mon, Nov 8, 2010 at 3:57 AM, Dr.
private final static String[] pqrLineStartRecords =
{ Pqr, REMARK 1 PQR };
Jmol is expecting:
REMARK 1 PQR file generated by PDB2PQR (Version 1.1.2)
REMARK 1
REMARK 1 Forcefield Used: AMBER
REMARK 1
REMARK 5
REMARK 6 Total charge on this protein: 4. e
So lacking that, yes,
looks like it's working great to me. Don't forget to add {1 1 1} before it:
load polymer.out {1 1 1} supercell {3 3 3}
Bob
On Wed, Nov 10, 2010 at 7:20 PM, pieremanuele canepa pc...@kent.ac.ukwrote:
Hi Bob,
could you check if the supercell option works for slab and polymers?
Thanks, Piero
Jonathan, Angel? Do either of you know why there are so many static fields
in WebExport? I'd like to make them nonstatic.
--
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
protected. I may
have time to look at the code this afternoon. Any module in particular?
Jonathan
On Nov 12, 2010, at 7:36 PM, Robert Hanson wrote:
Jonathan, Angel? Do either of you know why there are so many static fields
in WebExport? I'd like to make them nonstatic.
--
Robert M. Hanson
I'm not seeing the problem with 12.1.23_dev. If a carbon is sp2-hybridized,
as indicated here by the planar geometry, Jmol will correctly not add H
atoms to that position. The correct load if you want to convert 2D to 3D is:
load sample1.mol FILTER 2D
This will attempt to add hydrogen atoms and
2010/11/14 Angel Herráez angel.herr...@uah.es
load sample1.mol FILTER 2D
So that's what I have to use everytime, then?
Yes, because otherwise Jmol assumes you mean those are 3D, not 2D
coordinates.
How can I do that with jmolLoadInlneScript() ? I am not lading from file,
but from a
Héctor,
The best way to do this would be to include Jmol in your project as a
JmolViewer object and use that API. But if you want to do this from scratch,
look at the src/jmol/jvxl directory, which is the origin of all the
surfaces. src/jmol/jvxl/readers/IsoSolventReader.java creates the protein
Very important to use the UNSIGNED applet, I think, by the way. Just too
much the signed applet could do in a Wiki environment.
--
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
Piere, could you please try something for VASP OUTCAR? Try creating a file
with about 20 atom types and see what that does -- if it wraps to a new line
and causes a problem or if it doesn't wrap and works. Thanks.
Bob
On Mon, Nov 29, 2010 at 1:41 PM, Robert Hanson hans...@stolaf.edu wrote
fixed for Jmol 12.1.26 and Jmol 12.0.25.
On Wed, Dec 8, 2010 at 10:06 AM, Dr. Christoph Gille
christoph.gi...@charite.de wrote:
Thsi might be a possible bug?
After zap command the context menu becomes unavailabel.
How to reproduce:
Start Jmol from command line like
./jmol
public String getModelNumberDotted(int modelIndex)
On Wed, Dec 8, 2010 at 10:19 AM, Dr. Christoph Gille
christoph.gi...@charite.de wrote:
When refering to a specific molecul in Jmol I need the model number.
I mean the number which I use in selections like ... and 3.1 where 3 is
the model
go ahead and do that, Angel.
2010/12/13 Angel Herráez angel.herr...@uah.es
I realize that certain localizations are still in an immature state,
but if the JmolApplet0_i18n_pl.jar file is included in the
distribution and the 'language =pl ' command is available and
accepted, shouldn't that
Well, we aren't exporting SD files, just MOL files. Let's just implement an
SDF file writer and do that right rather than faking it.
2010/12/16 Angel Herráez angel.herr...@uah.es
I have found out that MOL files exported by Jmol, using the write
command, fail to be
opened in PowerMV, a free
Ah, you are too quick for me! I wasn't done.
See latest installment.
-- read/write SDF files (SDF)
-- read/write V2000 files (MOL or V2000)
-- read/write V3000 files (V3000 or atomno 999 or bondno 999)
Check it out.
Bob
2010/12/17 Angel Herráez angel.herr...@uah.es
Hi Bob,
I've looked
Nico, those need to be entered in Unicode format, not like that, I think.
Bob
2010/12/17 Angel Herráez angel.herr...@uah.es
Hi Nico
I have got your changes but now I cannot build Jmol locally; I get these
messages:
Do you have any tips? My local building using Eclipse is not something
I see -- Angel, update the full Jmol, not just the src. You need a new
project settings file.
On Fri, Dec 17, 2010 at 4:36 PM, Robert Hanson hans...@stolaf.edu wrote:
Nico, those need to be entered in Unicode format, not like that, I think.
Bob
2010/12/17 Angel Herráez angel.herr...@uah.es
got it -- and notice that now Jmol automatically converts 2D V3000 files
into 3D. See Jmol-dataFiles/mol/alanine.2D.v3000
On Fri, Dec 17, 2010 at 4:49 PM, Nicolas Vervelle nverve...@gmail.comwrote:
Hi Bob,
Several errors in unit tests.
**
junit.framework.AssertionFailedError: Error
If you look in that SPT file, you will see a
DATA coord set
block.
2010/12/17 Angel Herráez angel.herr...@uah.es
Bob, the doc
http://chemapps.stolaf.edu/jmol/docs/#writemodel
says
In the case of SPT, a script file containing the coordinates of the
model.
How is that? Only the state
Ah, sure. I missed that. This means you are up late on a Friday night.
Hmm
2010/12/17 Angel Herráez angel.herr...@uah.es
(Sorry I sent this to the wrong thread: localizations)
Bob, the month is wrong (zero-based)
__Jmol-12_11181000533D 1 1.0 0.0 0
should be
to test those V2000 files to see if they really do load
into that viewer.
Bob
On Fri, Dec 17, 2010 at 8:40 PM, Robert Hanson hans...@stolaf.edu wrote:
Ah, sure. I missed that. This means you are up late on a Friday night.
Hmm
2010/12/17 Angel Herráez angel.herr...@uah.es
(Sorry I sent
org.jmol.script.ScriptEvaluator - 5014 - instructionDispatchLoop
org.jmol.script.ScriptEvaluator - 230 - evaluateCompiledScript
org.jmol.viewer.Viewer - 4326 - evalStringWaitStatus
org.jmol.viewer.Viewer - 4091 - evalFile
On Sat, Dec 18, 2010 at 12:07 AM, Robert Hanson hans...@stolaf.eduwrote
I downloaded the OpenBabel GUI, and it read the V3000 file created using
load =1crn
write V3000 1crn.mol
and the very latest little fix I just checked in -- there was an extra 0
on the bond records.
One hitch was that
write 1crn.v3000
didn't work, because apparently OpenBabel requires a
Great, then I think we are all set. We will recommend using
write V3000 t.mol
rather than
write t.v3000
and we will not mess with
write t.v3000.mol
How's that? Then it is just the way it is with all the file writing.
write t.mol
and
write V2000 t.mol
are identical now -- V2000 will be
OK, no time to work on this today, but maybe tomorrow. If you get to
Orlando, and go to Disney World, please check out the Touch a Molecule
exhibit in the Innoventions building.
On Mon, Dec 20, 2010 at 4:49 AM, pieremanuele canepa pc...@kent.ac.ukwrote:
Dear Bob
I commit a new Java class to
Piere, can you please upload a set of Quantum Espresso files into
Jmol-datafiles? Thanks.
Bob.
ps -- too much snow coming down; decided not to risk driving out of town
On Mon, Dec 20, 2010 at 11:15 AM, pieremanuele canepa pc...@kent.ac.ukwrote:
hi Riccardo,
I am italian too. So Next time
I made some changes. I'm not optimistic, though --
* Problems identified (Bob Hanson) --
*
* -- Are these lattice vectors for the primitive unit cell? I think so.
* Then, if that's the case, why do we not see a list of
symmetry-generated atoms?
*
* -- Frequency data number of atoms
That was because I thought the atoms would be there -- like Crystal09 -- in
the primitive cell. Like I said, if that isn't the case, then we could go
back to reading the space group, but that has serious issues if the atoms
have to be generated by symmetry operators. It can't be done generally
?
---
From: Robert Hanson[SMTP:hans...@stolaf.edu smtp%3ahans...@stolaf.edu]
Sent: Tuesday, December 21, 2010 1:40:46 PM
To: P.Canepa
Subject: Re: FW: [Jmol-developers] gulp class
Auto forwarded by a Rule Piere,
sure -- If I have to put back in the conventional cell information, I will
-- I just
:
---
From: Robert Hanson[SMTP:hans...@stolaf.edu smtp%3ahans...@stolaf.edu]
Sent: Tuesday, December 21, 2010 5:04:37 PM
To: jmol-developers@lists.sourceforge.net
Subject: Re: [Jmol-developers] gulp class
Auto forwarded by a Rule I think we are going to have
structure.
hmm, my mistake. Should be reading them both.
Thanks, Piero
On Tue, Dec 21, 2010 at 6:58 PM, P.Canepa pc...@kent.ac.uk wrote:
---
From: Robert Hanson[SMTP:hans...@stolaf.edu smtp%3ahans...@stolaf.edu]
Sent: Tuesday, December 21, 2010 6
I see, so you need the intermediate stage, not the actual model. one problem
was that openClientFile was a misnomer -- clearly the actual file by then
is long closed. Where are you getting the AtomSetCollection from? Also, do
you have some reason to check the AtomSetCollection first? Part of the
...@gmail.com wrote:
On Fri, Jan 14, 2011 at 10:54 PM, Robert Hanson hans...@stolaf.edu
wrote:
I see, so you need the intermediate stage, not the actual model. one
problem
was that openClientFile was a misnomer -- clearly the actual file by
then
is long closed.
Indeed.
Where are you getting
Just a warning -- I spent much of the weekend rewriting sections of the Jmol
code for better handling of Jmol script arrays. I think I was pretty
careful, but it was quite involved, and you might get a null pointer
exception or especially a class-cast exception in 12.1.31_dev. I THINK it's
all
I hope someone is filing a bug report with Chrome -- you have a good page
there that very easily demonstrates the problem, it sounds like.
2011/1/28 Angel Herráez angel.herr...@uah.es
Not sure what's going on.
Jmol.js in inserting an applet tag (Jmol #1) for Chrome and fails to
display, but
Jonathan, can you send me one of those zip files?
On Sat, Jan 29, 2011 at 8:39 PM, Jonathan Gutow gu...@uwosh.edu wrote:
I'm looking for suggestions of things to look for. Within the SAGE math
package I use a state script generated by the applet that I have saved as a
string to recreate the
between 12.0.28 and 12.0.30? I didn't see a note about
fixing the misplaced semicolon, although I see it is correct now.
Jonathan
On Jan 30, 2011, at 7:20 PM, Robert Hanson wrote:
Jonathan, can you send me one of those zip files?
On Sat, Jan 29, 2011 at 8:39 PM, Jonathan Gutow gu
On Wed, Feb 2, 2011 at 12:56 PM, Jonathan Gutow gu...@uwosh.edu wrote:
Cool. What conference exactly?
http://www.icsti.org/spip.php?rubrique49
I did slip that semicolon in somewhere along the way there. So if
this is your problem, maybe somehow your JavaScript is stripping all
the
, Feb 3, 2011 at 7:38 PM, Jonathan Gutow gu...@uwosh.edu wrote:
On Feb 3, 2011, at 2:52 PM, Robert Hanson wrote:
On Wed, Feb 2, 2011 at 12:56 PM, Jonathan Gutow gu...@uwosh.edu wrote:
Cool. What conference exactly?
http://www.icsti.org/spip.php?rubrique49
I did slip that semicolon
You have to make sure you use ; if the script is to be part of the applet
tag. Simple \n line terminations will not work,and you cannot just load a
model using the DATA command this way.
textareas are WAY BAD ideas, because different browsers (historically at
least) treat the line endings
;
On Sun, Feb 6, 2011 at 2:07 AM, P.Canepa pc...@kent.ac.uk wrote:
---
From: Robert Hanson[SMTP:hans...@stolaf.edu]
Sent: Sunday, February 06, 2011 2:06:48 AM
To: jmol-developers@lists.sourceforge.net
Subject: Re: [Jmol-developers] very weird
Right, the XYZ format doesn't have atom names. It's main advantage is that
you can have an unlimited number of atoms. How about another format? Maybe
CML? The format is just about as simple as XYZ; a bit more verbose. id
should be atom name. You could then add bonds if you want.
?xml version=1.0
The Jar file is just a zip file. Check it to see that you have actually
included org/jmol/api/JmolAdapter.class
On Fri, Feb 18, 2011 at 1:17 AM, bobim zeynep.kosalo...@googlemail.comwrote:
Hi All,
I've written a small Applet that has the JMolPanel embedded. When I run the
applet in
please do ...
On Mon, Mar 7, 2011 at 7:24 AM, LANCASHIRE,Robert J
robert.lancash...@uwimona.edu.jm wrote:
Hi,
The reader for jaguar output files does not seem to be working for version
7.7
When I try to display the vibrational frequencies calculated by Jaguar the
info seems corrupt.
I'm starting to use Spartan Student, and I'm already a bit frustrated. Does
anyone know how to display a list of MOs in pictorial and energy form?
What do people think of another WebMaker option that would create an HTML
page the lists all the MOs for a system in order of energy in a table, with
I'm thinking more on the sophomore organic level than the physical chemistry
level. Seems to me it's pretty simple -- just need to get those PNG images
created and into the WebMaker folder. Could be not too many lines. I have
two trips to make in the next two weeks -- which reminds me -- anyone
Thanks, Angel. Any reason not to just clear all the users and start over?
2011/3/11 Angel Herráez angel.herr...@uah.es
Hi all
Today I've started some cleaning up of the user list in Jmol Wiki
(BTW we are still having spam user and page creation despite Nico's recent
preventive
measures)
The Finnish business is something having to do with the translation not
being complete or problems loading that, I don't know. Nico, you were
working on that.
The Edit/Select problem was that there are two menus with the same name (the
other under Display), and the name is saved in a Hashtable,
after bob fix for
the Select menu.
I have just released 12.0.38 and 12.1.41 is on its way.
Can you tell if you still see a problem ? If so, explain exactly what you
are seeing.
Nico
On Thu, Mar 24, 2011 at 6:40 AM, Robert Hanson hans...@stolaf.edu wrote:
The Finnish business is something
mouse xy is intrinsically 2D, not 3D. What are you thinking you might get
out of the x,y coordinates that would be 3D?
On Tue, Apr 19, 2011 at 6:58 AM, Eleazar Matheus
materias200...@gmail.comwrote:
Hi everyone,
I've been looking for a method that converts the mouse's (x,y) coordinates
to
Christoph -- How are you?
I finally tracked this down and realized I never answered your questions.
Sorry for that.
I don't see the shift-mouse-press being hijacked. Shift seems to still do
zoom and rotate, not selection. But there should be a way to do what you
want. You might look into some
got it! See http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
2011/5/14 Angel Herráez angel.herr...@uah.es
Under a particular situation I am finding that animation of a multimodel
file is blocked by
using hermiteLevel
This is a molecular dynamics trajectory fileset (topology
There you go - that's it! #2. Just use the code at
http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolPopup.htm
I think it's as easy as opening that page from the original with the ?SIGNED
option on the command line.
Bob
2011/6/18 Angel Herráez angel.herr...@uah.es
Hi Jonathan
I have
You can do that, but we are very close to not doing any more bug fixes in
12.0. I'd like to release 12.0 in mid to late July.
On Wed, Jun 29, 2011 at 1:42 PM, Jonathan Gutow gu...@uwosh.edu wrote:
I vote for bug-fix and inclusion in 12.0
Jonathan
On Jun 29, 2011, at 1:35 PM, Angel Herráez
I mean 12.2
On Wed, Jun 29, 2011 at 4:15 PM, Robert Hanson hans...@stolaf.edu wrote:
You can do that, but we are very close to not doing any more bug fixes in
12.0. I'd like to release 12.0 in mid to late July.
On Wed, Jun 29, 2011 at 1:42 PM, Jonathan Gutow gu...@uwosh.edu wrote:
I vote
I returned NAM and ASF for 12.1 -- I suggest they be returned for 12.0 as
well.
NAM is *N*-acetylmuramic
acidhttp://en.wikipedia.org/wiki/N-Acetylmuramic_acid
ASF is N-GLYCOSYL CHAIN
Was there some reason you were considering these not to be carbohydrates,
Angel? The reason to include them is
I'm working on adding hydrogens. That's been in there for simple models,
what I did today was set that up for amino acid and nucleic acid polymers.
Seems to be working OK, but just a warning for heads up -- there were some
problems with selecting groups after adding hydrogens. I think I've got
well, the molecular coordinates are just the molecular coordinates. This
slicing is by them, right? Not the screen coordinates? There are three
coordinate systems:
-- molecular coordinates
-- relation of those by rotation to the original view (the orientation
quaternion/matrix)
-- translation
By the way, you asked about the possibility of duplicating an isosurface so
there was a translucent shadow. Since rendering is a two-pass system, a
better way...
... to do that might be to set a flag to render the translucent pass without
slab and the opaque one with. Something on that order
Don't get me wrong -- I'm totally supportive of this effort. I just got
mixed up because I didn't realize that PDB had a different name for NAM than
what biochemists all know as NAM (AMU). So that was missing. Here's an
example (probably of no more than 8 examples total) of where NAM is NAM:
!--
On Thu, Jun 30, 2011 at 8:50 AM, Jonathan Gutow gu...@uwosh.edu wrote:
So I am still at my original question, which is will the boundbox
coordinates always be parallel to the molecular coordinates?
Yes, the bounding box is in molecular coordinates. So except for the
ghosting -- which I
If you are doing this in JavaScript, I would grab the state script and strip
out the isosurface command from it that was used (we could add some comments
to define it's first and last lines exactly), change the ID, and then run it
as an inline script; if doing this in Java, you have access to any
Jonathan,
On Thu, Jul 14, 2011 at 3:32 PM, Jonathan Gutow gu...@uwosh.edu wrote:
Based on what I can find in the code here are my options:
1) Modify getShapeProperty to include a getStateCmd option. Sounds simple,
but I find this access method strange as it duplicates methodologies built
.
We need to coordinate with Jonathan. I'd prefer if you at least did the main
changes. You have to do the changes manually, right? So something like
SHAPES will be quite the overhaul. I want to be on vacation when you do
that! :)
Nico
On Wed, Aug 3, 2011 at 11:18 PM, Robert Hanson hans
that's taken care of. Sorry about that!
On Wed, Aug 3, 2011 at 5:44 PM, Jonathan Gutow gu...@uwosh.edu wrote:
The mo command now sends Jmol into limbo.Not sure what happened.
Jonathan
Dr. Jonathan H. Gutow
Chemistry Department
I took a whack at this and found one bug even. Hopefully introduced no more.
But it does feel right. There are some instances, such as with the axesMode
and with proteinStructure where we need to have an integer ID still and
refer to that because that is documented as being exposed.
Very
and the PALETTE_...
constant, but not otherwise.
We just have to make absolutely sure we are not running through Enum
value()s just to get some information that is more easily saved in
constants.
Take a look. Check performance.
Bob
Nico
On Sat, Aug 6, 2011 at 5:20 PM, Robert Hanson hans
Hmm. This is a major issue. We have a way around this:
set numberFormatLocalization FALSE
but that's not going to solve the problem.
The Java method that is used to process this is the same one that is used
for many many aspects of Jmol. This is just one example of where that might
be a
OK, let's let it ride for now. But I see in the code that it SHOULD be a
problem!
2011/8/29 Angel Herráez angel.herr...@uah.es
Sorry, I am unable to reproduce this problem now, in 12.2.RC5
I will repost if it happens again.
Mario,
Fantastic!
You might be interested in knowing that a few years back Jmol was completely
compatible with non-Swing applications, but we opted for integrating Swing
completely when we moved to Java 1.6 (sorry about that!). Let's get your
work onto SourceForge as an android branch and see
:50 PM, Robert Hanson hans...@stolaf.edu wrote:
Mario,
Fantastic!
You might be interested in knowing that a few years back Jmol was
completely compatible with non-Swing applications, but we opted for
integrating Swing completely when we moved to Java 1.6 (sorry about that!).
Let's get your
On Mon, Sep 19, 2011 at 9:14 PM, Moacyr Francischetti corrêa
moa...@spacnet.com.br wrote:
Gentlemen,
2) The problem I have now is to keep this version synchronized with the
subsequent Jmol release versions (I used 12.1.13). Is there any way to
achieve this synchronism?
All depends on
var state = jmolGetPropertyAsString(stateInfo)
...
jmolScript(state)
2011/9/23 Angel Herráez angel.herr...@uah.es
Jonathan, I'm trying to use this idea of replacing the applet with
the signed vesion on request.
Coud you share the scripts you use for retrieving the state and
applying ti
(fileNameOrFlag) {
_jmol.archivePath =
(typeof(fileNameOrFlag) == string ? fileNameOrFlag : (fileNameOrFlag
? JmolAppletSigned : JmolApplet) + 0.jar);
On Sep 23, 2011, at 4:24 AM, Robert Hanson wrote:
var state = jmolGetPropertyAsString(stateInfo)
...
jmolScript(state)
2011/9
I get it.
2011/9/23 Angel Herráez angel.herr...@uah.es
What's the goal of JmolToSigned?
Looks to me like it just returns a file name.
It **assigns** a file name to the _jmol.archivePath variable. This
allows the page to destroy an applet and replace it with the signed
applet.
Or
Over the past few days I've been doing some major refactoring of Jmol 12.
The changes should be transparent, but the overall effect should be
significant.
All core java.awt and java.swing references are now made from within
org.jmol.awt or org.jmol.export (where all the file dialogs are).
Oh, oh. Nothing was refactored between those. I wonder what happened. Let me
take a look.
OK, I'm guessing that when I moved popup and console to org.awt, that is
what did it. But I'm surprised that it couldn't just track those same
phrases to different places.
Nico, we may need your expertise
, at 10:55 AM, Robert Hanson wrote:
Over the past few days I've been doing some major refactoring of Jmol
12. The changes should be transparent, but the overall effect should be
significant.
All core java.awt and java.swing references are now made from within
org.jmol.awt
here.
Dean
On Tue, Sep 27, 2011 at 2:02 PM, Jonathan Gutow gu...@uwosh.edu wrote:
This looks cool...I'm going to see if I can convince my School to set
something up.
Jonathan
On Sep 27, 2011, at 10:55 AM, Robert Hanson wrote:
Over the past few days I've been doing some major refactoring
my School to set
something up.
Jonathan
On Sep 27, 2011, at 10:55 AM, Robert Hanson wrote:
Over the past few days I've been doing some major refactoring of Jmol
12. The changes should be transparent, but the overall effect should be
significant.
All core java.awt and java.swing
that's fixed.
2011/10/1 Angel Herráez angel.herr...@uah.es
I just tested kiosk mode in latest 12.2_dev at StOlaf
The instructions at the top say to type exitJmol but this is not
recognized with that case; all
lowercase exitjmol does close the kiosk
version=12.2.0
Documentation is pretty much all there:
http://chemapps.stolaf.edu/jmol/docs/
# 224 new features (see
http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/viewer/Jmol.properties?view=markup
)
# summary of feature changes between Jmol 12.0 and 12.2:
# FEATURE
remember why I thought that was a good idea.
Maybe because there is no color relative?
Bob
Oliver
On Sat, Oct 1, 2011 at 16:57, Robert Hanson hans...@stolaf.edu wrote:
version=12.2.0
Documentation is pretty much all there:
http://chemapps.stolaf.edu/jmol/docs/
# 224 new features (see
Oh, that's right! I thought Nico had straightened that out, but maybe not. I
will look into it later today. So let's hold on this for now.
2011/10/2 Angel Herráez angel.herr...@uah.es
Have we got the translation issue sorted out for this release?
I mean, that bunch of new untranslated phrases
# ANDROID BRANCH (for Mario Kosmiskas mar...@uw.edu)
version=12.2.0_A
# All java.awt and java.swing references are now isolated.
# Two key packages to take a look at are:
#
# org.jmol.api.ApiPlatform -- a class that must be instantiated by
org.jmol.viewer.Viewer
# using reflection. To do
I've given a little more detail about the CONTACT command at
http://chemapps.stolaf.edu/jmol/docs/index.htm#contact
Except for elaborating some more on that, I'm done adding documentation, so
if you see something I forgot, do let me know.
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf
I'm testing an option for parallel module loading. If you are interested,
please help by letting me know if there is any significant difference
between:
1) clear JAVA cache (Windows control panel...Java...temporary internet
files...select all...delete
2)
The problem is that every time we do that to an established phrase we will
lose all current defiinitions --- unless we had a way to update the current
.po files so that
#: org/jmol/console/ScriptEditor.java:135
msgid Top
msgstr Subir
becomes
#: org/jmol/console/ScriptEditor.java:135
msgid
browser
3) http://chemapps.stolaf.edu/jmol/docs/examples-12/test_load2.htm
reported time: _ s
(because I guess the browser also caches the Jar files separately from Java,
so both caches have to be cleared).
Thanks,
Bob
On Mon, Oct 3, 2011 at 7:06 PM, Robert Hanson hans...@stolaf.edu wrote:
I'm
The trunk is now 12.3, headed for 12.4
Jmol 12.2 is now a branch and is closed to development but still open to bug
fixes
Jmol 12.0 is closed to all developments and bug fixes
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
I've at least put in the [] business (starting or end of line) for Jmol
12.3.1. I saw there was one already in there anyway.
2011/10/4 Angel Herráez angel.herr...@uah.es
In my opinion, being able to make distinctions between phrases that
translate different. There are a few other instances
that there is still some caching going on since the very first
load of load1 took 26.9 sec...
On Oct 4, 2011, at 5:24 AM, Robert Hanson wrote:
OK, that's changed a bit:
1) clear JAVA cache (Windows control panel...Java...temporary internet
files...view...select all...delete
2) close and reopen browser
do empty the cache, and reset website data before I quit and restart
Safari...
René
On Oct 4, 2011, at 2:45 PM, Robert Hanson wrote:
can you use the other ones I sent in a separate message -- shouldn't be
using that applet at all.
The files I'm using are in
http://chemapps.stolaf.edu/jmol
I have a feeling Safari is not playing nice and is not clearing its cache.
Ignore that! How about Firefox?
On Tue, Oct 4, 2011 at 3:29 PM, Robert Hanson hans...@stolaf.edu wrote:
So can you start with 2 and do #1 in reverse?
On Tue, Oct 4, 2011 at 2:41 PM, Kanters, Rene rkant
On Oct 4, 2011, at 6:09 PM, Robert Hanson wrote:
I have a feeling Safari is not playing nice and is not clearing its cache.
Ignore that! How about Firefox?
On Tue, Oct 4, 2011 at 3:29 PM, Robert Hanson hans...@stolaf.edu wrote:
So can you start with 2 and do #1 in reverse?
On Tue, Oct 4
sure. But you may want to keep them as separate frames and just display
both frames. This is nice, because it allows you to more easily select one
or the other independently.
load files protein.mol2 ligand.mol2
On Fri, Oct 7, 2011 at 6:32 AM, Sam Paul D. reachsamp...@gmail.com wrote:
hi,
I
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