Oh my. I had forgotten about this. If you actually open Bob's Jmol model
kit mode, turn the substrate pink:
set modelKitMode;set selectHetero on;select hetero;color pink
and use the drag (shift to rotate) commands to move the substrate
slightly out of place, then the drag/minimize command will
Those I have are very big. I zip two of them OUTCAR_MD.zip under vasp test. 6
Mb I hope they are not too big.
Piero
--
Please consider the environment before printing this e-mail.
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of
Hi Alexander and Bob-
I'm going to go out on a limb here and say that I think Alexander wants
to do something that's not as complex as it seems. While my description
below uses the links on my page, I am really just using Jmol's model kit
mode commands.
I'll use lactose permease (courtesy of
That's going to rotate the atoms about a specific molecular axis. Do you
want it to rotate about a specific window axis, regardless of how the model
is oriented? Is that the problem? There might be a way of doing that with
quaternions.
On Mon, Nov 8, 2010 at 12:39 PM, Alexander Rose wrote:
> Hi
I just solved a big problem. It can be a warning to you. My Safari
(5.0.2 in OS 10.5.8) has been acting very badly: links often don't
work, Proteopedia green links never work, it crashes often, hangs now
and then, etc. etc.
A week or so ago I installed a couple of extensions in Safari. One
wa
Can you deposit a sample MD file, so I can see how that works?
On Mon, Nov 8, 2010 at 12:20 PM, P.Canepa wrote:
>Can you add this change yourself because. I am confuseed at a certain
> point. You had moe experience.
> You find the last revision in the trunk.
> By the way can you help me? wit
Alexander,
I'm still a little confused about your objective. Try this. Go to:
http://chemagic.com/web_molecules/script_page_large.aspx
Click the Molecular Editor link. Click "duplicate." There are now two
models in the window. Click "move." After you click "move," either model
can be click/dr
Hi Otis,
Am 08.11.2010 um 20:22 schrieb Otis Rothenberger:
> Hi Alexander-
>
> I'm not sure exactly what you want to do, but if you want to
> independently translate or rotate non-bonded models, or rotate about a
> given bond (i.e. conformation rotation), then there is a really simple
> way t
Hi Alexander-
I'm not sure exactly what you want to do, but if you want to
independently translate or rotate non-bonded models, or rotate about a
given bond (i.e. conformation rotation), then there is a really simple
way to do either of these.
1) With one or more models in the same window, the
Hi,
>From the manual
"set allowRotateSelected FALSE
When set TRUE, this parameter allows user rotation of the molecule containing
the selected atom using the mouse (holding ALT down while dragging). The
coordinates of the rotated molecule will be sightly degraded in this process."
I would li
Can you add this change yourself because. I am confuseed at a certain point.
You had moe experience.
You find the last revision in the trunk.
By the way can you help me? with the question I asked
Thanks, Piero
--
Please consider the environment before printing this e-mail.
Pieremanuele Canepa
R
I did it nothing happens.
--
Please consider the environment before printing this e-mail.
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
e-mail: pc...@kent.ac.uk
mobile: +44 (0) 7772
Shoot ah I forgot..
--
Please consider the environment before printing this e-mail.
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
e-mail: pc...@kent.ac.uk
mobile: +44 (0)
Try using JmolApplet.jar instead of JmolApplet0.jar
2010/11/8 Angel Herráez
> Might be something with my system, but I am seeing it at both
> computers, and with different applets (Jmol unsigned, my campus
> Blackboard environment, among others). Also in different browsers.
>
> The warning jumps
Piero, by the way, did you move that setAtomSet() call back to where it
needed to be?
On Mon, Nov 8, 2010 at 10:18 AM, P.Canepa wrote:
> Dear Bob,
>
> something weird is happening. Today i recompiled the developer version of
> Jmol with the new features for VASP me and Bob had recentely introdu
Piero, it sounds like a java cache problem. The browser may be
reading the old applet files from cache instead of the new ones
coming form the server.
Make sure that you close your browser, clear your java cache and
restart the browser
---
Dear Bob,
something weird is happening. Today i recompiled the developer version of Jmol
with the new features for VASP me and Bob had recentely introduced.
In local all the new VASP features do perfectly work. Once I upload Jmol on my
web page http://j-ice.sourceforge.net/ondemand/index.html
Angel, et al-
I don't know if this is relevant, but when I had the problem with
1.6.0_22, I saw a number of blogs, including one at Oracle, that
indicated a cookie problem related to security and 1.6.0_22. I was in a
hurry trying to track down a Jmol issue, so I did not want to take the
time t
Might be something with my system, but I am seeing it at both
computers, and with different applets (Jmol unsigned, my campus
Blackboard environment, among others). Also in different browsers.
The warning jumps most often saying it's jmolApplet0.jar, but some
times it has been another componen
On 11/08/2010 03:48 PM, Robert Hanson wrote:
> I have just upgraded to Java 1.6.0_22 with Windows 7 and with XP and find no
> such problem.
> So let's think about this some more. What could Angel's problem be?
>
> My test was to load
>
> http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm
>
I have just upgraded to Java 1.6.0_22 with Windows 7 and with XP and find no
such problem.
So let's think about this some more. What could Angel's problem be?
My test was to load
http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm
and also
http://chemapps.stolaf.edu/jmol/docs/examples-12/s
2010/11/8 Angel Herráez
> Yes, I am seeing it with the unsigned applet (sorry I failed to
> mention this important bit initially)
>
> oh, that's not good news. Really? Then this has to be a bug report to
Oracle. You sure about that?
> And it doesn't seem to be dependent on the Jmol version, bu
Yes, I am seeing it with the unsigned applet (sorry I failed to
mention this important bit initially)
And it doesn't seem to be dependent on the Jmol version, but I
haven't checked that systematically
After playing with the Java Control Panel options the warning is
gone, but I chose one of the
On 11/08/2010 02:46 PM, Angel Herráez wrote:
> Thanks, Otis
> I think that what you mention is a different issue. I also saw some
> changes in security rules related to paths some time ago.
> But this says it is the use of mixed signed and unsigned features
> **in the code***. I am speaking of th
Thanks, Otis
I think that what you mention is a different issue. I also saw some
changes in security rules related to paths some time ago.
But this says it is the use of mixed signed and unsigned features
**in the code***. I am speaking of the unsigned applet, that of
course is not supposed to h
Sounds like something we can handle when the signed applet JAR files are
created. I think
Trusted-Library: true
might work.
Nico?
Bob
2010/11/8 Angel Herráez
> This looks like a good explanation of how to fix this, both at user
> level and at developer level:
>
> http://download.oracle.co
Hi Angel-
While I did not get mix warning notices, I did get security violation
notices when I tried to use Jmol script to load files on my localhost
server. This started happening after I installed 1.6.0_22. I reinstalled
1.6.0_21 and the problem disappeared. I'll take a look at your
suggest
This looks like a good explanation of how to fix this, both at user
level and at developer level:
http://download.oracle.com/javase/6/docs/technotes/guides/jweb/mixed_c
ode.html
--
The Next 800 Companies to Lead Americ
Hello Jmol users
It's been several weeks now that every time I open a web page with
Jmol applet I receive a Java security warning saying that there is a
mixture of signed and unsigned content in the applet and requesting
permission to continue (in fact, recommending not to do so).
I'm quite su
29 matches
Mail list logo
