Have you submitted a bug report?
Sent from my iPhone
On Aug 16, 2013, at 10:48 PM, Robert Hanson hans...@stolaf.edu wrote:
Say, look at this: This is Safari figuring out the values of the numbers on
the line (x, y, then z):
ATOM 1241 CD1 LEU A 64 -2.206 36.532 31.576 1.00 60.60 C
but not the structure then the page became
unresponsive. When I tried the link for 1m19.pdb.gz it also gave an
unrecognized file format error.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan
I didn't time it, but both sites similar for me and around 10 seconds. Latest
Mountain Lion and Safari 6.0.2.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
, at least not in the several minutes
I waited.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Nov 28, 2012, at 2:33
get the non-recognized
format error.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Nov 28, 2012, at 2:33 PM
.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Nov 28, 2012, at 4:53 PM, Robert Hanson wrote:
yes, of course! Try now. Note that the density one
it back
and forth horizontally and the reflection moved with it, but when you moved
your hand up the reflection moved down. Seems kind of weird.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle
Yes. I like that better. Very nice. How would one make it so that if you
turn spinning on that is synced in this way too.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan
Is it possible to get those partial charges with more sig figs?
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
than bonds
they do not.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Apr 24, 2012, at 12:51 AM, Robert
No problem on my MacBook Pro with Safari. Tried both with Jmol unsigned and
ChemDoodle. Also fine with FireFox.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
with
ChemDoodle though not with Jmol and they are ball and stick. It looks
different on the iPod Touch. Not saying it is better or worse, just not the
same behavior. I figured you all would like to know how it compares.
***
Jeff Hansen
Department
Not seeing that behavior on my Mac.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Apr 24, 2012, at 12:02 PM
.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Apr 13, 2012, at 10:43 AM, Robert Hanson wrote:
Phil -- the OK prompt is just
It is in the link he provided.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Apr 5, 2012, at 10:36 AM, Philip
?
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Apr 3, 2012, at 3:46 PM, Robert Hanson wrote:
I think this question got lost
Assuming everyone wants to spend $20 for a Windows only application I suppose
you might be right (about not putting it at the top of the todo list).
Probably not a good assumption though.
***
Jeff Hansen
Department of Chemistry and Biochemistry
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Feb 10, 2012, at 12:20 PM, Robert Hanson wrote:
frank off
I just did too. Didn't realize what it was when I replied before. Just struck
me that frank off could be some way of telling someone off. Didn't know it
meant that. Hope I didn't offend.
***
Jeff Hansen
Department of Chemistry and Biochemistry
I'm not sure where your problem is, but look here for a solution to this.
Perhaps it will help you with yours. Bob Hanson also has a nice solution.
http://web.me.com/jhansen4/iWeb/Jmol/svgGraphTest5.xhtml
***
Jeff Hansen
Department of Chemistry
Its a start. Still a long way to go.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Sep 13, 2011, at 10:16 PM
Whatever the problem is I don't think you can blame it on Safari. All three
links are fine for me in Safari 5.1, OS 10.6.8. No error messages in the
console.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College
Would it be possible to add an invisible atom in front of the protein and
rotate the protein until the distance from the selected residue to the
invisible atom is minimized?
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
so my name must be
correct!
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Apr 22, 2011, at 1:34 PM, Otis
Or perhaps also a canvas tag object.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Apr 17, 2011, at 6:56 AM
{
var applet=_jmolGetApplet(targetSuffix);
if (applet) applet.script(script);
}
}
Any suggestions on what I'm doing wrong?
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
?
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
The problem does not occur when the students are working in their own local
folders. What I showed you was all that I deleted - just text within a pre
/pre tag.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S
. Thought it was weird.
Just glad I don't have to open each html file and delete stuff.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
for a two finger tap and
drag or some other dragging with a key down.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
read)
load C6H6.smol
script ERROR: java.security.AccessControlException: access denied
(java.util.PropertyPermission http.agent read)
load C6H6.smol
Anyone else have a similar experience?
***
Jeff Hansen
Department
Ah yes. I remember the Firefox issue now. Glad it isn't just me.
Tracked down the offending extension. It is AdBlock. I'm reluctant to turn it
off, but I guess I'll have to - at least when I'm using Jmol.
***
Jeff Hansen
Department of Chemistry
so I can't see it well
except for when scrolling.
Jeff
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Aug 16
{atomIndex = _atomPicked};
}
set PickCallback jmolscript:klick();;
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
that.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Jul 27, 2010, at 7:20 AM, Philip Bays wrote:
Wow. I find it hard
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Jul 25, 2010, at 11:24 AM, Robert Hanson wrote:
OK, I've tested this on my Mac with a freshly
.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Jul 25, 2010, at 1:14 PM, Philip Bays wrote:
Bob:
Several answers and a comment. The signed applet always
Sorry, not sure where to find that. I cleared them from the Firefox Tools menu.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Jul 24, 2010, at 10:32 AM, Robert Hanson wrote:
also, Phil, you will need to be very specific
Works fine now on both Safari and Firefox.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Jul 24, 2010, at 11
Nope. NT1 gives the access denied error. NT2 works fine.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Jul
Firefox version is 3.6.8
Java version is 1.6.0_20
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Jul 24, 2010
/
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Jul 17, 2010, at 4:36 PM, Robert Hanson wrote:
OK. Got it! Whew
Can you imagine the response you would have received even just 5 years ago if
you had complained because your phone didn't do Java? I would guess that in
another 5 years or so the response will be similar.
***
Jeff Hansen
Department of Chemistry
that? Is there
any hope of ever achieving a stable cross browser, standards-based solution
that won't require relearning a new system?
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Jul 1, 2010, at 12:37 PM, Robert Hanson wrote:
about Spartan --
I guess I'll stick with
http
you already
know how to do that. I could show you, but I'm leaving town tomorrow so it
would have to wait until I get back.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan
. Probably possible, but I'm not sure exactly how
to do it.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Jun 30, 2010
Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Jun 30, 2010, at 2:09 PM, Pshemak Maslak wrote:
On 6/30/2010 10:38 AM, Jeff Hansen wrote:
OK. So ignore my previous
Same for me with Mac Mail.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Jun 1, 2010, at 10:10 PM, rgb wrote
Wow!!
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On May 27, 2010, at 10:30 PM, Robert Hanson wrote:
I have
.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On May 21, 2010, at 12:03 AM, Robert Hanson wrote:
Mac-side bug fixed. Please do check this out:
http
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Apr 27, 2010, at 1:32 AM, Otis Rothenberger wrote:
Jeff,
Your notes
Depicting the carbocation back to JME does reveal it to be a boron.
Reloading that back into Jmol shows it as a pretty pink boron atom. Still not
planar, even after another optimize.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw
, it flattened out nicely.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Apr 26, 2010, at 9:24 PM, Philip Bays wrote:
I
I get a non-planar carbocation.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Apr 25, 2010, at 10:06 PM, Otis
and two-finger scrolling?
Even outside of using a MacBook Pro, I'm sure not everyone uses a scroll wheel.
Jeff
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
Still does not work with a trackpad.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Apr 15, 2010, at 8:19 AM
not sure why it is not
interpreting either of those actions as a left click so that it does the bind.
In all other cases that I have encountered either the trackpad click or the
double tap and drag work.
Jeff
***
Jeff Hansen
Department of Chemistry
Otis,
'Tis a thing of beauty. Works wonderfully, either way (option double tap or
option two finger tap).
Jeff
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
All three of the links on that page worked for me on Mac OS X 10.6.3 and Safari
4.0.4. However, when I tried to drag a pdb file from a Finder window, I got a
FileNotFoundException.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw
the other? By
simple I mean with mouse actions. I know it could be done via the console.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
All worked fine for me, including drag and drop of multiple files from multiple
folders in Finder. On Firefox 3.6 and OS X 10.6.3.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
How about hovering over the bond instead of atoms, or at least a single click
on the bond instead of having to click two atoms.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan
believe would all be done outside
of Jmol using javascript (to rewrite the trajectory file) then tell Jmol to
reload the trajectory file. Is that what you need?
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College
If the applet were within a div of defined size would the size of the div stay
the same and thereby keep the applet the same size? Don't know but thought
maybe this could be a solution?
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw
How about selecting aromatic rings or different functional groups?
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
. The molecule was strange in that it was completely flat
with several atoms overlapping. I don't know if that is how the structure
should be, but it looked very odd.
Hope this helps.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602
Forgot to mention this was with Safari 4.0.4. Pretty much the same behavior in
Firefox 3.5.6.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
make it that much more
useful.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Jan 9, 2010, at 4:57 PM
Very nice!
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Jan 2, 2010, at 4:35 PM, Jonathan Gutow wrote
. Starting a new SourceForge project would
not preclude continuing to use it in Jmol.
Jeff
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
retrieved.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Dec 16, 2009, at 5:35 PM, rgb wrote:
It detracts from
I've seen this before too - I believe in .mol files output from Spartan.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
we want to adjust? Kind of a built in
slider.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Nov 18, 2009
there. Some mouse-over prompt as Bob
suggested would be good in addition to that.
Jeff
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
of consistency and over time things
will seem more intuitive.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Oct
On Oct 20, 2009, at 12:08 PM, Robert Hanson wrote:
And about the Mac interface, there's lots of help to get started
either with the system help or with online tutorials. Once you get
started I think you'll find lots of consistency and over time things
will seem more intuitive.
The
- just a slightly different color or lighter shade - would
lead people to think it was a menu, which it is.
Jeff
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
but then it wouldn't be so obvious that it is a menu. Like
I said, I haven't seen David's suggestion. It might work fine. I do
think having it in the top left is more likely to trigger one to think
it is a menu.
***
Jeff Hansen
Department
Is there somewhere I can see what file types Jmol can read and what
the format of each of those file types is?
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
a single value of 0.06260959.
Any ideas what I'm doing wrong here?
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
be desirable or is this something better left not done?
Jeff
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
It may be that there is a problem, but I don't see it on my computer
which is a MacBook Pro running OS X 10.5.8 and using Safari 4.0.3.
The animation runs smoothly throughout.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw
be
a better solution than a new window. Hope this helps.
Jeff
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Jun 4, 2009, at 1:22 PM, Angel Herráez wrote:
Hello nmckenna
As far
any help anyone could
provide to take this further.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
an onclick=circle_click(evt) within the tag for the circle
element in the svg.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
not.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
the corresponding point in the graph. Still need
axes and some other niceties but I'm pretty sure the code to do that
is out there somewhere so I'll put that in next week.
http://web.me.com/jhansen4/iWeb/Jmol/JmolPlusSVG.xhtml
***
Jeff Hansen
Department
Great. Will do. Thanks.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On May 19, 2009, at 4:12 AM, Angel
someone point me in the direction of how to make changes in
the applet trigger an event?
http://web.me.com/jhansen4/iWeb/Jmol/JmolPlusSVG.xhtml
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle
this and/or how to fix it I would appreciate
hearing it.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
. Is this the intended
behavior?
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On May 8, 2009, at 12:52 AM, Robert Hanson
of the summer too.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On May 8, 2009, at 8:19 AM, Robert Hanson wrote:
Jeff
overkill since its just for looks. I've thought about trying to
do it somehow with bezier curves. Any suggestions?
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
not work there as its implementation of SVG is poor to
non-existent. I don't see a way around that and frankly standards are
there for a reason so as long as my code is standards compliant I'll
be ok with that.
***
Jeff Hansen
Department
not sure why, but since it seems to be necessary I did it.
Jeff
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On May
affect html pages.
I can't currently test IE8. My understanding is that the svg would
require a plug-in from adobe. Not sure about xhtml.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
as a problem?
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On May 7, 2009, at 12:01 AM, Robert Hanson wrote
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