Hi Charles,
You need to update your JSmol.
This bug has been fixed in Jmol/JSmol 13.2.6:
bug fix: chains improperly selected in JSmol/HTML5
(you are still running 13.2.4)
Best,
Oliver
On Fri, Nov 15, 2013 at 9:11 PM, Charles Gasser csgas...@ucdavis.eduwrote:
Help!
I am trying to select
Hi,
The jsmol.zip that I have just downloaded seems to be broken:
$ unzip jsmol.zip
Archive: jsmol.zip
End-of-central-directory signature not found. Either this file is not
a zipfile, or it constitutes one disk of a multi-part archive. In the
latter case the central directory and
Hi Bob,
I just discovered Nullpointer with set allowRotateSelected TRUE in Jmol
13.1.13
Cheers,
Oliver
Exception in thread AWT-EventQueue-11 java.lang.NullPointerException
at
sun.plugin2.main.client.DetachedAppletController.appletImplementsDragging(Unknown
Source)
at
Hi,
How important is it that the molecule is completely within the ellipsoid?
I have seen the use of the inertia equivalent ellipsoid to characterize
molecules.
e.g. MDanalysis [1] calculates the principal axes from the moment of
inertia [2].
The resulting eigenvectors can be used to construct
There was an actively used zero-day exploit in Java 7 that made Apple and
Mozilla to black-list the Java 1.7.0_10 plugin:
[1]
http://www.h-online.com/security/news/item/Java-plugins-unplugged-by-Mozilla-and-Apple-Update-1782628.html
However today Oracle has released an update fixing that issue:
First of all: JSmol is a really GREAT idea and I am still stunned how
good it works.
One question: do pickCallbacks work with JSmol as well?
Up to now I haven't seen a demo with pickCallbacks and right now I
don't have time to try myself, but next year I'm going to start a
project where I'll
On Nov 24, 2012, at 6:52 PM, Oliver Stueker wrote:
First of all: JSmol is a really GREAT idea and I am still stunned how
good it works.
One question: do pickCallbacks work with JSmol as well?
Up to now I haven't seen a demo with pickCallbacks and right now I
don't have time to try myself
Hi,
the security issues with Java 1.7 also apply to the 1.6 series [0,1].
Fixes of three critical vulnerabilities in 1.7.0_7 and 1.6.0_35 at least
stop publicly available exploits, but sill contain several other holes [2].
Still afaik Java 1.7.x is (a bit) more secure than 1.6.x [0].
Oliver
Thanks Bob!
I can confirm that
ISOSURFACE iso1 PLANE {0 0 1 -15 } WITHIN 3.0 {protein} MAP property_correl
works in general but the mapping is weird (iso_1step.jpeg)
But thankfully
ISOSURFACE iso2 PLANE {0 0 1 -15 } MAP property_correl
ISOSURFACE SLAB WITHIN 3.0 {protein}
produces the result
Hi Bob,
I just noticed that write image seems to be broken in Jmol 12.3.30:
$ write image test.png
JPG64
$ write image test.jpeg
JPG64
12.3.29 still worked.
Oliver
--
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Exclusive live
Great!
Thanks a lot Bob!!!
Best,
Oliver
On Fri, Jun 15, 2012 at 4:14 PM, Robert Hanson hans...@stolaf.edu wrote:
see http://chemapps.stolaf.edu/jmol/Jmol-12.zip
On Fri, Jun 15, 2012 at 5:03 PM, Robert Hanson hans...@stolaf.edu wrote:
Oliver,
It's a bug. I can stop that from crashing,
Is there any way to map the potential of custom atom-properties to a
planar (square) isosurface as a color gradient?
Oliver
On Fri, Jun 8, 2012 at 6:12 PM, Oliver Stueker wrote:
Hi Jmol-Community,
it seems I am again kind of stuck. :-/
I have some correlation data for a protein (1 value
) are ignored by
ISOSURFACE PLANE MAP.
(with Jmol 12.2.28, 12.3.28)
Is this intended behavior?
Best,
Oliver
On Thu, Jun 14, 2012 at 12:07 PM, Oliver Stueker
revilo2...@users.sourceforge.net wrote:
Is there any way to map the potential of custom atom-properties to a
planar (square) isosurface as a color
Hi Jmol-Community,
it seems I am again kind of stuck. :-/
I have some correlation data for a protein (1 value per residue) that
I want to map on different isosurfaces.
I have succeeded in mapping the data on Molecular (or VDW, SAS)
surfaces, but now I am interested how things look like inside
Hi,
unfortunately Jmol under Linux has become some sort of an issue since
Oracle changed their license and now won't allow the Linux distributions to
include Oracle-Java binaries anymore and as Angel correctly pointed out,
the IcedTea Java plugin is not compatible with Jmol.
But for all you
I think I've cracked it:
If I use RANGE as part of the ISOSURFACE command, it seems to have no effect
load $caffeine
calculate partialCharge
isosurface vdw map mep color range -1.0 1.0
isosurface vdw map mep color range -0.1 0.1
but after that I can modify the color gradient with the COLOR
On Thu, May 24, 2012 at 2:26 PM, Alexander Rose alexander.r...@weirdbyte.de
wrote:
Hi,
Am 24.05.2012 um 20:37 schrieb Oliver Stueker:
Still I think an option to let Jmol generate a legend for the applied
gradient would be a nice feature.
like 'set isosurfacekey on;' ?
Best
Alexander
Hi Bob,
I see. Actually I forgot to use the MAP keyword (actually it seems to be
implied when I use property_xxx).
and I can also confirm that
ISOSURFACE my_iso1 VDW COLORSCHEME bwr COLOR RANGE -1.0 1.0 property_xxx
works (even without MAP) but
ISOSURFACE my_iso1 VDW property_xxx COLORSCHEME
On Wed, May 23, 2012 at 11:42 PM, Oliver Stueker
revilo2...@users.sourceforge.net wrote:
Hi,
I get an NullPointer when trying to write a PNGJ in Jmol 12.3.26.
$ write IMAGE PNGJ my_image.png
script ERROR: ERROR creating image??: java.lang.NullPointerException
write image
iso_sas2 select { protein } only saSurface 1.4
property_xxx within 1.0 colorScheme user color range -1.5 1.5
Thanks,
Oliver
[1] http://chemapps.stolaf.edu/jmol/docs/examples-12/new2.htm?topic=53
On Tue, May 22, 2012 at 5:44 PM, Oliver Stueker
revilo2...@users.sourceforge.net wrote:
This time
:
isosurface1 created with cutoff=0.0; isosurface count: 1
isosurface full data range -0.15823531 to 0.130531 with color scheme
spanning *-0.1 to 0.1*
On Wed, May 23, 2012 at 3:56 PM, Oliver Stueker
revilo2...@users.sourceforge.net wrote:
Hi,
I have the impression that ISOSURFACE ... COLOR
Hi,
I get an NullPointer when trying to write a PNGJ in Jmol 12.3.26.
$ write IMAGE PNGJ my_image.png
script ERROR: ERROR creating image??: java.lang.NullPointerException
write image pngj my_image.png
$
In version 12.3.25 writing PNGJ works and there are no problems writing a
at 4:45 PM, Daniel Carbajo daniel.carb...@gmail.comwrote:
I have the following embedded in a jmol button and works perfectly:
jmolButton(write image.png, Create image);
Cheers,
Daniel
2012/5/24 Oliver Stueker revilo2...@users.sourceforge.net
Hi,
I get an NullPointer when trying to write
Oliver Stueker revilo2...@users.sourceforge.net
A simpler example:
on http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm (12.3.27_dev
2012-05-23)
load caffeine.mol
calculate partialCharge
isosurface vdw map mep color range -1.0 1.0
isosurface vdw map mep color range 0.0 1.0
isosurface
This time sending from the correct address. ;-)
-- Forwarded message --
Hi Bob and other fellow Jmol'ers,
When I run the following commands in Jmol 12.3.25:
{protein}.property_xxx = data(load(data_file.dat),1,0,1 );
set userColorScheme deeppink white green ;
isosurface
Hi Sara,
which version are you using? I can't reproduce that with 12.3.12 and 12.2.12.
With this script everything looks normal:
set pdbaddhydrogens ;
load=1H6I ;
cpk off ; wireframe on ;
select [TYR]227:A OR [ALA]232:A ;
wireframe 0.15 ; cpk 25% ;
center selected ;
zoomto 1 (selected) 500;
Angel,
That is really great!
I can confirm it works on Linux (Ubuntu 10.4.3 LTS Lucid) with
sun-java 1.6.0_26 and
* Chrome 14
* Firefox 3.6.22
It only failed when I tested the very first time short after you sent
the email (with Chrome)
Probably because the signed Applet wasn't in my
Hi,
Is there any possible location of a script file that the
Jmol-Application would automatically evaluate when starting? (Similar
to, say, an .bashrc)
I guess not, at least I couldn't find anything the documentation (main
website, wiki or scripting doc).
I would really like to pre-define a
Hi Yingjie,
Yes, on this list one can really learn a lot about JmolScripting and
combining this with other web techniques.
On Fri, Mar 25, 2011 at 15:18, Yingjie Lin yingjie@mssm.edu wrote:
Hi Bob,
Your answer is very thorough. My problem is solved. More importantly, I
learned a lot
itself to pass data back to the server.
Just use the load() function in Jmol script. No need for AJAX with that.
Remember, AJAX was designed with JavaScript in mind, not Java. Java already
has the capability to communicate with your server.
Bob
On Tue, Mar 22, 2011 at 5:21 PM, Oliver
Hi Yingjie,
keep in mind that the Jmol Applet is executed inside the Browser of
the user whereas your python script runs on the webserver.
So you'll need to communicate data from the client back to the server.
The first step would be passing the data that you need from the
Java-Applet into the
to
labels.
version=12.1.35_dev
version=12.0.32_dev
# bug fix: {xxx}.label = xxx does not allow saving state
# bug fix: {xxx}.element = B only assigns B to first atom in set
Bob
On Wed, Feb 9, 2011 at 11:36 AM, Oliver Stueker
revilo2...@users.sourceforge.net wrote:
Hi Bob,
to reproduce
Hi,
Though I mentioned to this issue before, it's probably better to start
a new thread for this:
When I load a molecule with an embedded jmolscript to the
Jmol-application directly via the command line, the embedded script is
not executed.
for example:
I take caffeine.xyz from
jmolscript: embedded
scripts
see http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
On Thu, Feb 10, 2011 at 2:56 PM, Oliver Stueker
revilo2...@users.sourceforge.net wrote:
Hi,
Though I mentioned to this issue before, it's probably better to start
a new thread for this:
When I
; # changes only N2 to carbon
Cheers,
Oliver
On Wed, Feb 9, 2011 at 07:11, Robert Hanson hans...@stolaf.edu wrote:
I'll need that file. hans...@stolaf.edu
On Mon, Feb 7, 2011 at 3:54 PM, Oliver Stueker
revilo2...@users.sourceforge.net wrote:
Hi Bob, Nico,
Thanks for the fast response
that got lost. It's fixed in 12.1.34
and 12.0.31, which I hope Nico can release later today.
On Fri, Feb 4, 2011 at 4:51 PM, Oliver Stueker
revilo2...@users.sourceforge.net wrote:
Hi,
I just noticed that the element assignment via atom properties is
broken in Jmol 12.0.30:
{*.?H??}.element=1
Hi,
I just noticed that the element assignment via atom properties is
broken in Jmol 12.0.30:
{*.?H??}.element=1 ; # fails
{*.?H??}.element=H ; # fails
while it still works for individual atoms:
{atomno=2734}.element=1 ; # works
In Jmol 12.0.28 it still worked.
Oliver
Hi Bob,
just noticed you have submitted a fix in the SVN.
I can confirm that branches/v12_0/Jmol at Revision: 14672 does the trick for me.
Thanks a lot!
Cheers,
Oliver
On Mon, Nov 15, 2010 at 12:34, Oliver Stueker
revilo2...@users.sourceforge.net wrote:
Hi Bob,
First, thanks for fixing
Hi Bob,
First, thanks for fixing the file-dropper for Linux - works great now!
Second,
You probably have missed my bug-report that I had posted in the same thread:
I found another minor Unix/Linux specific bug:
When using the (tab) command-auto-completion in the Jmol Console to load a
file
and therefore under Linux
(or any other OS with case-sensitive file-system) the load fails.
Thanks,
Oliver
On Tue, Oct 26, 2010 at 16:46, Oliver Stueker
revilo2...@users.sourceforge.net wrote:
Hi,
The path is correct except of the \r\n .
(where the backslashes in case of the png is also
Hi Bob,
Just a small bug that I noticed the other day (not urgent, just that
it won't get missed):
Under Linux (Ubuntu 10.04 Lucid Lynx, Gnome 2.30.2) I can't load files
via drag-and-drop:
for a png I get:
script ERROR: io error reading
file:/home/stuekero/Desktop/myFile.png/r/n:
:
Oh, is it just the CR LF at the end?
On Tue, Oct 26, 2010 at 4:29 PM, Oliver Stueker
revilo2...@users.sourceforge.net wrote:
Hi Bob,
Just a small bug that I noticed the other day (not urgent, just that
it won't get missed):
Under Linux (Ubuntu 10.04 Lucid Lynx, Gnome 2.30.2) I can't load
Thanks Bob!
That helped a lot, though I'm not quite there yet.
On Thu, Oct 21, 2010 at 06:59, Robert Hanson hans...@stolaf.edu wrote:
Oliver,
Great to see people picking up on this power of quaternions. It's easier
than you think.
Well, they're still ~50% black magic to me. :-)
1)
Hi,
I wonder, is there a way in Jmol to control the order of the atoms
within a selection?
What I want to do:
--
I have a geometrical (polyhedral) structure with triangular faces in
file1.pdb and a triangular plane
with a few chains attached to it on one side (roughly
Hi Bob,
On Thu, Sep 9, 2010 at 23:58, Robert Hanson hans...@stolaf.edu wrote:
This one is for Rich, Eric, Jay, Sergio, and Oliver.
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
[...]
version=12.1.11_dev
# new feature: lockMultipleBonds (preliminary)
# set
Hi,
I just noticed that Jmol 12.0.11 writes PDB files that don't match to the
specification.
for example: (col header for orientation)
1 2 3 4 5 6 7
8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
HETATM
Hi,
with Jmol 12.0 you can use the following Jmol Script command:
load SMILES Oc1ccc(cc1)C3(OC(=O)c2c23)c4ccc(O)cc4
(see: http://chemapps.stolaf.edu/jmol/docs/?fullmanual=1ver=12.0#k428 )
That works for me with the Application. On a webpage you probably need
to use the signed Applet.
(see:
-users
--
Oliver Stueker
Post-doctoral Fellow, Theory and Modeling Group
NRC-NINT / University of Alberta, Canada
--
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit
Hallo Alexander,
On Mon, Feb 22, 2010 at 14:40, Alexander Rose
alexander.r...@weirdbyte.de wrote:
Hi all,
maybe someone can help.
I have an atomno, that I can select with 'select ({3})'. Now but I want to
select the residue the atom is belongs to. Is that even possible?
select
-on, but disabling it for a
certain site or server works for me.
Maybe it helps.
Oliver
--
Oliver Stueker
+-++
| University of Paderborn | Office: J6.302 |
| Faculty of Science | phone: +49 (5251) 60-2498
(as the Fox and java were quite outdated)
OS: SUSE Linux 10.1
Browser: MozillaFirefox-2.0.0.10-0.2
Java:java-1_5_0-sun-1.5.0_14-0.1
java-1_5_0-sun-plugin-1.5.0_14-0.1
for latter I needed to create a new Firefox-profile.
And it worked well.
Oliver
--
Oliver Stueker
) on
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
with the C6H6.smol from the server.
* Windows XP SP2
* Java 1.6.0_03 and 1.5.0_13 (only Application 11.3.38)
* Firefox 2 in case of applets
Oliver
--
Oliver Stueker
this:
connect (_c and within(1.6, coord, {0 0 0})) aromatic modify;
for good results (_c for carbon; add the word coord explicitly)
Bob Hanson
Oliver Stueker wrote:
Hi, i want to report a possible bug:
When I load e.g. a benzene molecule (like attached benzene.xyz) and
then submit
to period and also give up A4 Paper if US
completely changes to the metric system. :-)
Oliver
--
Oliver Stueker
+-++
| University of Paderborn | Office: J6.302 |
| Faculty of Science | phone: +49
.
Especially as I get the values with commas when I don't use
pformat-syntax. (label %x gives 0.1234, label %5.4x gives 0,1234)
Thanks in advance
Oliver
--
Oliver Stueker
+-++
| University of Paderborn | Office: J6.302
, Firefox 1.5.0.3, Sun Java JRE 1.5.0_06
Jmol and JavaScript console are both empty.
For content of the JavaConsole see attachments.
Oliver
--
Oliver Stueker
+-++
| University of Paderborn | Office: J6.302 |
| Faculty
(visibility):
It says set hydrogen ON/OFF, which doesn't work.
(should be set showHydrogens on/off)
...Oliver
--
Oliver Stueker
+-++
| University of Paderborn | Office: J6.302 |
| Faculty of Science | phone
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