Hi,
Google analytics can filter bots and spiders
https://plus.google.com/+GoogleAnalytics/posts/2tJ79CkfnZk
Andreas
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https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/ha
etected as a “hover."
>
> Otis - AKA Oits ;>)
>
> --
> Otis Rothenberger
> o...@chemagic.org
> http://chemagic.org
>
> On Mar 21, 2016, at 7:23 PM, Andreas Prlic wrote:
>
> I confirm, there is a problem with access from Safari.
>
> We (RCSB) already
ser setting. Also, on the RSCB REST site:
>
> http://www.rcsb.org/pdb/software/rest.do
>
> Their local REST test on that page was up and down for me on Sarai during
> several tests today.
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.org
> http://chemagic
Hi,
RCSB is up and running. http://status.rcsb.org/
I also tested from http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm and all
seems be running fine from there.
Can you access the RCSB web site in your browser? Perhaps there is a
networking issue. Also: do you see a stacktrace in your javascript
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Hi,
I am trying to get the latest jsmol to work without the default
jmolApplet0_query _select and _submit user interface components. When I use
Jmol.setDocument(0) and
addSelectionOptions(false);
there are uncaught TypeErrors in JSmol.js (OSX chrome)
infotablediv and appletdiv have no style,
I'm running Jmol 12.0.22 through BioJava.
> We need to get BioJava gurus to move to Jmol 13. (Andreas? Peter?) Maybe
> there is a newer version of BioJava than what you are using.
>
>
Good point. - I upgraded the BioJava to the latest Jmol version that is
available from Maven central - 13.0.10. Ha
seems all fine on my FF4.0.1 also on Chrome (11.0.696.71)
Andreas
On Mon, May 30, 2011 at 10:08 AM, Philip Bays wrote:
> Bob:
> All work fine in Safari, though I had to clear the browser cache and history
> to get it to do so.
> Phil
> On May 30, 2011, at 12:54 PM, Robert Hanson wrote:
>
> I've
The javascript error console is empty. (no errors, no warnings, no messages)
A
On Mon, May 30, 2011 at 9:17 AM, Robert Hanson wrote:
> looking for the JavaScript error console. Can't remember how you do that on
> a Mac
>
-
says, that would be helpful.
> Sounds to me like this browser has no access to java.lang.System
>
> Also -- I notice that with MSIE 9 you can no longer enter javascript
> commands this way on the URL line. Anybody know a work-around for that?
>
> Bob
>
>
> On Mon, May 30,
> Progress. What does your computer report when you issue this on the URL
> input line of your browser:
>
> javascript:alert(java.lang.System.getProperty('java.version'))
This does not give any response.
Andreas
--
vRang
sorry for the long mail, I am trying to describe all related details:
it happened yesterday when I followed the link that you posted to your site
http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm?topic=71
However I can;t seem to reproduce this today. (it does not happen
every time) From o
I meant to say I am NOW getting a javascript alert, sorry for the typo...
Andreas
> I am on firefox 4.0.1 (osx) and on many sites that are using jmol I am
> not getting a "Your web browser is not fully compatible with Jmol",
> although Jmol usually works fine.
>
> I suppose Jmol.js needs to be up
Hi,
I am on firefox 4.0.1 (osx) and on many sites that are using jmol I am
not getting a "Your web browser is not fully compatible with Jmol",
although Jmol usually works fine.
I suppose Jmol.js needs to be updated to know about FF4.x ?
Andreas
--
I see. Any chance to be able to influence the color for the frank in
this case? The red clashes with my other color choices...
Thanks,
Andreas
On Fri, Mar 25, 2011 at 12:34 PM, Robert Hanson wrote:
> yes, that's right. A bit of a security feature -- I want to know if the
> applet I'm looking at
Hi,
I was just playing around with turning the "frank" of Jmol off. It
seems it currently can be turned off in the unsigned version of the
applet, but not in the signed version (both 12.0.37). Is this the
expected behavior?
Thanks,
Andreas
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Senior
:
> On 11/17/2010 08:42 PM, Andreas Prlic wrote:
>> Ok here my suggestion for a palette that resolves to various
>> distinguishable shades of blue and yellow for color blind people and
>> still looks kind of ok-ish for all others (thanks to
>> http://colorschemedesigner.com
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a part of the beta today
> http://p.sf.net/sfu/msIE9-sfdev2dev
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on the web. Be a part of the beta today
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oys/colors/
Thanks,
Andreas
--
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 85
I am using the feature to automatically fetch the map from the EDS server:
isosurface "=3NO8" ; color isosurface yellow
if the restriction could be done on a map that already has been loaded
that would be great, since the download is very slow
Thanks,
Andreas
2010/11/2 Angel Herráez :
> Hi
Hi,
I am just playing around with using Jmol to show electron density
maps. Is there a way to restrict the display of the map to a certain
atom-set ? Slab seems to work, but when I just want to see the surface
around a certain residue "restrict isosurface" does not seem to do
anything. "isoSurface
ple.htm, and you can
> see there that =3cdz loads just fine and displays just fine.
>
>
> Bob
>
>
>
> On Fri, Oct 15, 2010 at 1:00 PM, Andreas Prlic wrote:
>
>> Thanks for the quick update,
>>
>> now I am getting a different exception. This one has been p
/chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12_0.zip
>>
>> On Thu, Oct 14, 2010 at 6:49 PM, Andreas Prlic wrote:
>>
>>> Hi,
>>>
>>> I just tried to upgrade our Jmol installation to 12.0.18 (binary
>>> download), but I noticed the following
ure; color structure; select ligand;wireframe
0.16;spacefill 0.5; color cpk ; select all; set antialiasDisplay true;
Can you take a look?
Thanks,
Andreas
--
-------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Dat
priate pdb file in Proteopedia's Scene authoring tools and
> paste into the console the state script from elsewhere (with load command
> commented out) and save the resulting scene to your page with the data
> residing on Proteopedia's server.
>
> Wayne
>
>>Date: S
Related to this I was wondering if it is possible to upload the state
of Jmol to a server. This could be similar to saving the state
locally, but rather than writing the file, Jmol could post the state
to a URL provided by the web site...
Andreas
On Sun, Aug 8, 2010 at 2:23 AM, Egon Willighagen
If I am right, the Pymol align command does a sequence alignment followed by
a superposition of atoms.
http://www.pymolwiki.org/index.php/Align
I am not a big friend of naming discussions, just trying to help avoid
future questions ... ;-)
Andreas
On Mon, Mar 15, 2010 at 9:29 AM, Robert Hanson
Could you give the new command a different name? ALIGN is misleading since
you are not doing an alignment, but just a superposition.
http://en.wikipedia.org/wiki/Structural_alignment
Thanks,
Andreas
On Mon, Mar 15, 2010 at 6:05 AM, Robert Hanson wrote:
> Kersten,
>
> I have had some success in
one set to the other via an optimized rotation and translation.
>
> That's what you are interested in, right Kersten?
>
> Bob
>
> On Wed, Mar 10, 2010 at 12:47 PM, Andreas Prlic wrote:
>
>> no, protein only...
>>
>>
>> On Wed, Mar 10, 2010 at 10:
no, protein only...
On Wed, Mar 10, 2010 at 10:43 AM, Robert Hanson wrote:
> Ah, that's useful information, Andreas. Does it also work with nucleic
> acids?
>
> On Wed, Mar 10, 2010 at 12:11 PM, Andreas Prlic wrote:
>
>> Hi,
>>
>> We are using Jmol to vis
Hi,
We are using Jmol to visualize protein structure alignments as part of the
RCSB PDB Protein Comparison Tool.
http://www.rcsb.org/pdb/workbench/workbench.do
It contains the Combinatorial Extension (CE) algorithm (among others), which
is a frequently used algorithm for protein structure alignme
Hi Cihan,
I have the same problem with a checkout from trunk.
Reason is a bug in the setAppletContext method. Solution is to add the
following line of code to org.jmol.viewer.Viewer in the method
setAppletContext
if ( commandOptions == null)
commandOptions = "";
2009/6/4 Cihan Öğüt :
>
>
Hi Jeff,
Now sure what's exactly the problem from your description, perhaps you
can send some example code?
We are using a mix between JQuery and self written javacript on the
new RCSB-PDB web site:
e.g. this page tracks the Jmol console output to a div and shows the
command history:
http://www.
1.0 844 -487 225 116.6;
OR
#Follows Z-Y-Z convention for Euler angles
reset; rotate z 140.0; rotate y 112.0; rotate z -100.0;
Andreas
-------
Andreas Prlic Wellcome Trust Sanger Institute
pository - should be fixed
there.
Andreas
> -------
Andreas Prlic Wellcome Trust Sanger Institute
Hinxton, Cambridge CB10 1SA, UK
some threading issues I would vote for setting the
default to ON.
Andreas
-------
Andreas Prlic Wellcome Trust Sanger Institute
Hinxton, Cambridge CB10 1SA, UK
---
Andreas Prlic Wellcome Trust Sanger Institute
Hinxton, Cambridge CB10 1SA, UK
+44 (0) 1223 49 6891
---
This SF.Net email is
Hi!
Is there actually a way to say something like
select 10-20 ; set helix true ; select 20-30 ; set strand true;
?
Thanks!
Andreas
---
Andreas Prlic Wellcome Trust Sanger Institute
Hi Egon!
SpartanModel Jmol
Commerial yes no(t yet)
Does this meant there are plans to form some kind of business around
Jmol?
Cheers,
Andreas
---
Andreas Prlic
3.2.2
Don't have latest version installed, so can not test.
btw- the demo scipt on www.jmol.org seems to end with statically
displaying "jmol". Perhaps it would be nice to start from beginning
after a while?
Cheers,
Andreas
--
------
A
Congratulations!
very nice work! Jmol rocks!
and nice demo-script on the homepage :-)
works perfectly with
firefox 1.0, konqueror 3.2.2 and
Java 1.4.2_05-b04 on debian
Andreas
--
--
Andreas Prlic Wellcome Trust Sanger Institute
Hi!
I just happened to browse through the PDB-beta web site and it seems to
also support Jmol now.
e.g
http://pdbbeta.rcsb.org/pdb/explore.do?structureId=1bpi
Thought you might be interested...
Andreas
--
--
Andreas Prlic Wellcome Trust
..
I added a couple of links to example code, how to integrate Jmol into an
application. I found Integration.java out of the Jmol CVS particularly
helpful :-)
Cheers,
Andreas
-
------
Andreas Prlic Wellcome Trust Sanger Inst
--
--
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Hinxton, Cambridge CB10 1SA, UK
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Thanks!
Andreas
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