Hi Jay,
I have the same problem because I stubbornly refuse to upgrade Java to
higher than 1.6.0_21. That's the last version that allows an applet to
access files via a localhost server for development.
Unfortunately, Chrome now has a feature that tries to force you to upgrade
Java versions. T
Hi guys, I can't get my jmol applets to run in google chrome, 1.6.24.
It just points me to the java download page (i.e. the yellow applet not
supported screen).
Any ideas for a fix ?
Works fine in firefox.
--
Jay Vyas
MMSB/UCHC
--
Paul,
I see the same thing. If I gently rotate a fragment, I can see that it's
translating as I rotate it. No matter which way I rotate, the translation is
always in the same direction - toward infinity. As you say, this behavior is
initiated by the rotate compare command.
Otis
--
Otis Roth
I've just made another try, with the same structure. Everything worked fine (I
could translate or rotate all molecules in every direction, and rotating with
the cursor outside an atom just moved the entire scene). But once I clicked on
the left column link with the "rotate compare" command, the
Bob and Paul,
I think that behavior has been there all along. On
the rotation, you must start with the cursor on an atom. Once you start
the rotation, you can move the mouse cursor away from the model, but it
must start on an atom. If you do not start on an atom, ZOOM takes
over. ZOM into
There is also a funny bug (in the biological meaning) with files such as 1gzx,
1hba (hemoglobin) where the proteins acts as spiders retained by their silky
strings to the hemes. But if the hemes are dragged, the whole corresponding
chain is actually dragged !
Le 6 mai 2011 à 21:09, Robert Hanso
Just like Bob said, on my Mac (10.6.7, Java 1.6.0_24) it depends on whether
it is the signed applet (or stand alone app). With the signed applet or
application, I find it handy to select text from the Jmol console (or the
script editor) and then click and drag it onto the desktop to create a "text
OK! I'll look into that. We don't want any molecules to escape.
On Fri, May 6, 2011 at 1:49 PM, Paul Pillot wrote:
> Well, I just tried to run the "set picking dragmolecule" command for the
> structures displayed at the link you gave and there is a strange bug when I
> try to rotate the molecule
Well, I just tried to run the "set picking dragmolecule" command for the
structures displayed at the link you gave and there is a strange bug when I try
to rotate the molecules independently (it happens at the second try) : the
molecules flies away in an unexpected direction (translation I suppo
Copying from the java console on a Mac (10.6 Safari) works fine for me. I can't
remember if I made a specific setup, but the java console opens automatically
when I load a webpage with an applet. Otherwise, you can probably call it via
the top menu bar coffee icon.
-Paul
Le 6 mai 2011 à 20:05,
again, the "workaround" is simply to copy from the Java console, not the
Jmol console. I know, with Macs that might be hard to find. Someone with a
Mac can fill us in on that. It looks like the Jmol console can only be
clipped from using the signed applet. I believe this is the intended
behavior of
FWIW I've also found problems copying states text from the console in the past
few days. I'm on Mac OS 10.6.x/Safari/Firefox/Chrome.
Unlike Angel I didn't find a workaround. I used the signed applet to save a
file which was why I asked about loading it on the fly.
All the best
Nick
--
3D Organic
Wayne -- I was mistaken, because all I tried to do was to clip it into the
input box. I didn't realize that Java had its own private clipboard.
Really, the solution is to clip from the Java console, not the Jmol console.
A bit of a drag on a Mac, I think, because it's hard to find, but that
should
Thanks, Wayne
I was quite sure I had read similar issues here, thoughtit was with
the Mac.
I cannot confirm if 1.6.0_24 was working or not for me. 25 is not,
and it's the first time I've noticed but there may have been several
updates in between.
Bob,
thanks, now I see that the output of "s
Hi Angel,
I recently developed the same/similar problem; copying from and pasting into
the
Jmol console the normal way failed on my Windows PC, in both Firefox and
Chrome.
Quite frustrating. However, it stopped working for me when the update was to
Java version 1.6.0_24. So it seems one earlie
ah, and I am mistaken! I cannot clip out of the console either.
I think if you look in the Java Console, whatever is shown in the Jmol
console is there as well. No need to execute it. Just clip from the Java
console, not the Jmol console.
Bob
On Fri, May 6, 2011 at 9:39 AM, Robert Hanson wrote:
that's disgusting! :)
2011/5/6 Angel Herráez
> I don't know if this was there in 1.6.0_24 (but I have used this way
> of getting orientation moveto many times before).
> I have now found a workaround:
>
> I'm using the unsigned applet script console.
> I select (mouse drag) what is in the upper
I don't know if this was there in 1.6.0_24 (but I have used this way
of getting orientation moveto many times before).
I have now found a workaround:
I'm using the unsigned applet script console.
I select (mouse drag) what is in the upper panel, output area; press
Ctrl-C, but it cannot be pasted
working with 1.6.0_24/Windows 7/Firefox; don't know about 1.6.0_25
2011/5/6 Angel Herráez
> I can no longer copy text output to the Jmol script console (like
> "show orientation")
>
> This seems to be related to the update of Java. I have just installed
> 1.6.0_25, under WinXP
>
> I think there
...and have them move smoothly back to where they were originally using
ROTATE COMPARE. See
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=114
On Fri, May 6, 2011 at 6:56 AM, Paul Pillot wrote:
> Set picking dragmolecule allows that too
> You can even move the different chains fr
I can no longer copy text output to the Jmol script console (like
"show orientation")
This seems to be related to the update of Java. I have just installed
1.6.0_25, under WinXP
I think there was recent discussion about this in MacOS. Any ideas
will be welcome
--
Set picking dragmolecule allows that too
You can even move the different chains from one molecule to put them apart !
I set up a page here : http://www4.ac-lille.fr/~svt/nucleotides/adn.htm to make
pairs with dna nucleotides
-Paul
Le 6 mai 2011 à 13:12, Alexander Rose a écrit :
> Hi,
>
> http:/
Hi,
http://chemapps.stolaf.edu/jmol/docs/?ver=12.0#setmisc
There is a command for rotation and translation each:
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).
Hello Reinhold
You are right, rotation, zoom etc. affects all frames/models.
The only way is to use the "rotateSelected" command. But that doesn't
work by mouse, only does defined angles.
I think there is no way to do interactive rotation of a single model.
--
At the moment I'm trying to load more than one molecule from multiple
pdb data files into one Jmol instance. It works fine using the load
append command, and I can display any of the loaded molecules separately
or all together.
But I can't seem to find any function that allows me to manipulate
25 matches
Mail list logo
