it in your script, and uploading the
'ported' page onto the new wiki?
Jaim
--
Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il
Head Bioinformatics|
RD Bioinformatics and Data Management |
Department of Biological Services |
Weizmann Institute
, and for choosing the clear 'global_' label
to avoid further confusions.
Best regards,
Jaim
--
Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il
Head Bioinformatics|
RD Bioinformatics and Data Management |
Department of Biological Services
=1blu
$ initialize
$ show variables
returns
# --no global user variables defined--;
Thank you again,
Jaim
--
Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il
Head Bioinformatics|
RD Bioinformatics and Data Management |
Department of Biological Services
Jmol (11.5.35 and 11.8.9) can't open PDB 3irj,
reporting this error:
script ERROR: Error reading file at line 192:
CRYST11.0001.0001.000 0.00 0.00 0.00 P 1 1
cannot invert matrix
Jaim
--
Dr Jaime Prilusky | jaime.prilu
to RCSB about this entry.
Jaim
--
Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il
Head Bioinformatics|
RD Bioinformatics and Data Management |
Department of Biological Services |
Weizmann Institute of Science | fax: 972-8-9344113
76100
is only a skeleton and might be
improved easily for batch conversion.
Jaim
--
Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il
Head Bioinformatics|
RD Bioinformatics and Data Management |
Department of Biological Services |
Weizmann Institute
Hi,
Is 'set rocketBarrels' working on jmol 11.8.24 ?
In general, is there an option to remove arrow heads?
(beta sheets, ...)
Thanks in advance,
Jaim
--
Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il
Head Bioinformatics|
RD Bioinformatics
According to Angel Herráez angel.herr...@uah.es:
'set rocketBarrels' is working OK for me in 11.8.23, 11.8.24, 12.0.RC11
and 12.0.RC15
Thanks a lot. Will try again.
Jaim
--
Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il
Head Bioinformatics
According to Robert Hanson hans...@stolaf.edu:
I'm happy to remove arrow heads from the boxes with
set rocketbarrels true
It seems that this only works on alpha helices, no effect on beta sheets.
Jaim
--
Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il
Head
Hi,
Two water related questions:
Is there an option for drawing water as crosses instead of spheres?
Is there an option to 'set autobond OFF' only for water?
Thanks,
Jaim
--
Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il
Head Bioinformatics|
RD
According to Angel Herráez angel.herr...@uah.es:
connect (water)(water) delete
Great, thanks. This works perfect.
Jaim
--
Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il
Head Bioinformatics|
RD Bioinformatics and Data Management |
Department
to .jvxl the surface alone ...
Can we combine both?
Or the option is to reload state and then load jvxl?
Thanks,
Jaim
--
Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il
Head Bioinformatics|
RD Bioinformatics and Data Management |
Department
According to Robert Hanson hans...@stolaf.edu:
write xxx.zip
Thanks,
Jaim
--
Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il
Head Bioinformatics|
RD Bioinformatics and Data Management |
Department of Biological Services |
Weizmann Institute
/wiki/some_script.php');
Both way work fine on Safari and on FFox on Mac 10.5
and the files can be read with FFox on SnowLeopard if
entered as URL on the browser.
Jaim
--
Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il
Head Bioinformatics|
RD
that the
bond is connecting to, but to the bond line itself.
If possible, then, can I attach a label to the selection?
Thanks in advance,
Jaim
--
Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il
Head Bioinformatics|
RD Bioinformatics and Data Management
by pairs
Thank you Angel for a useful suggestion,
Jaim
--
Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il
Head Bioinformatics|
RD Bioinformatics and Data Management |
Department of Biological Services |
Weizmann Institute of Science
Thanks Bob for a prompt reply.
Using 'script' instead of 'load' solved the problem.
Thanks again,
Jaim
--
Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il
Head Bioinformatics|
RD Bioinformatics and Data Management |
Department of Biological Services
and
downloadable pdf (just over 2 US$). See
http://stores.lulu.com/angel_herraez
--
Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il
Head Bioinformatics|
RD Bioinformatics and Data Management |
Department of Biological Services |
Weizmann Institute
On line 833 of the file Jmol.body.php remove the '' from the third parameter
of the function jmolTag()
Jaim
--
Dr Jaime Prilusky
Head Bioinformatics
RD Bioinformatics and Data Management
Department of Biological Services
Weizmann Institute of Science
76100 Rehovot – Israel
mail: jaime.prilu
and try to
make it work.
Jaim
--
Dr Jaime Prilusky
Head Bioinformatics
RD Bioinformatics and Data Management
Department of Biological Services
Weizmann Institute of Science
76100 Rehovot – Israel
mail: jaime.prilu...@weizmann.ac.il
tel: 972-8-9344959
fax: 972-8-9344113
OCA, http://oca.weizmann.ac.il
is required.
Best Regards,
Jaim
--
Dr Jaime Prilusky
Head Bioinformatics
RD Bioinformatics and Data Management
Department of Biological Services
Weizmann Institute of Science
76100 Rehovot Israel
mail: jaime.prilu...@weizmann.ac.il
tel: 972-8-9344959
fax: 972-8-9344113
OCA, http://oca.weizmann.ac.il
Kilian,
Please check access rights to the files.
It's clear that you can access Jmol.php and Jmol_body.php, since they're are
doing their job.
In the same directory you must have the COPYRIGHT.txt file and several others.
Unless your browser has access to those files, the applet will not
Killian,
On your test, try always to access a plain text, html or image file (.txt,
.html, .png, .gif)
Files ending on .php will get a different treatment on the server side and many
times you will be unable to see them from a browser.
Jaim
--
Dr Jaime Prilusky
Head Bioinformatics
RD
/selinux/enforce
And after testing Jmol, you can enable it again with
echo 1 /selinux/enforce
Jaim
--
Dr Jaime Prilusky
Head Bioinformatics
RD Bioinformatics and Data Management
Department of Biological Services
Weizmann Institute of Science
76100 Rehovot - Israel
jaime.prilu
(not the full
path) can be used to setup the internal default file path to the location of
the model file, and call the load.
Jaim
--
Dr Jaime Prilusky
Head Bioinformatics
RD Bioinformatics and Data Management
Department of Biological Services
Weizmann Institute of Science
76100 Rehovot - Israel
(ucfirst($name));
$fullPath = images/ . substr($md5,0,1) . / . substr($md5,0,2) . / .
ucfirst($name);
Jaim
--
Dr Jaime Prilusky
Head Bioinformatics
RD Bioinformatics and Data Management
Department of Biological Services
Weizmann Institute of Science
76100 Rehovot - Israel
eml: jaime.prilu
This is really something!!
It looks so smooth and simple :-)
Well done!!
On Apr 13, 2012, at 8:03 AM, Robert Hanson wrote:
OK. Please test!
http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
-- adds loading of host-local file using
MolGrabberJmol.loadFile(fileName,loadParams)
of course,
A server side script should work fine. Can you provide a URL to see what you
get?
Jmol + server side scripts that generate HTML on the flight are used on
numerous sites. A few examples
http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CTS
http://oca.weizmann.ac.il/oca-bin/ccpeek?id=2CTS
I'm counting on that. Please let me know if you need any help.
Jaim
On Apr 17, 2012, at 4:50 PM, Nicolas Vervelle wrote:
Hi,
I haven't really followed this discussion.
Can it be used for the MediaWiki extension ?
Nico
On Tue, Apr 17, 2012 at 3:33 PM, Paul Pillot
Maybe we don't need to invest too much on mmCIF support, and concentrate on the
upcoming PWF (wwPDB Working Format).
This might be the new format that (based on an undisclosed source), PDB is
seeking to get the crystallographic community approval on. When, how and if
this will happen is
Very nice!!!
And with label %[partialCharge] it looks great.
On May 8, 2012, at 11:04 PM, Robert Hanson wrote:
OK, this is working.
http://chemapps.stolaf.edu/jmol/docs/examples-12/simple2.htm
load a model by name from either PubChem or NCI
then click on the button on the right that reads
Dear Jane,
I just found out that we (Proteopedia's SAT) is the responsible for Jmol
displaying element information instead of the default phi,psi and omega values
on a Ramachandran plot.
Please hover points on
http://proteopedia.org/wiki/index.php/User:Jaime_Prilusky/Ramachandran_plot for
a
Dear Karl,
Take a look to the source of http://proteopedia.org/w/Forms_of_DNA
I would say that you are missing jmolSetTarget('A');
Jaim
On Jun 12, 2012, at 6:31 PM, Oberholser, Karl wrote:
Bob,
What is wrong with how I implemented your suggested code for the sync
command? My
Double check to ensure that you use the same URL on all pages. Changes like
additional 'www' will induce Java to think that you're accessing another server
and this is against the security rules.
Jaim
On Jun 18, 2012, at 3:30 PM, Martin Hediger wrote:
Dear Jmol Developers
I'm having a very
before you hit Initialize, so you see the error
message.
Thanks again and looking forward to any feedback.
Martin
On 18.06.12 15:15, Jaime Prilusky wrote:
Double check to ensure that you use the same URL on all pages. Changes like
additional 'www' will induce Java to think that you're
I will appreciate some examples on how to use 'bgyor' (Reverse Rainbow) color
gradient when coloring by temperature (working on Jmol 13.0.1).
On our tests, defaultColorScheme = rasmol; color temperature; still draws
using the standard Direct Rainbow gradient.
Thank you in advance,
Jaim
Dear Angel,
Thank you for a prompt, clear and accurate reply (as always :-)
Regards,
Jaim
On Sep 2, 2012, at 4:03 PM, Angel Herráez wrote:
Dear Jaim,
I find the doc for color-schemes misleading but then I have found a way; you
need to specify a property in order to use a color scheme.
$795 for 25 servers or applications!
http://p.sf.net/sfu/zoho_dev2dev_nov___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
__
Dr Jaime Prilusky
Head Bioinformatics
RD Bioinformatics
On Jan 25, 2013, at 9:00 PM, Jonathan Gough wrote:
At the moment, I am using the St. Olaf packages to trouble shoot the issues.
If I can't load a simple page that utilizes your code - then in my mind there
is an issue with the server I am using to host the single page, yes?
'loadScript' is
A fast, minimal JSmol, able to load additional features on demand, will be
great.
However, I think this will have little impact on model loading and management
speed. Is this correct?
Jaim
On Jan 30, 2013, at 8:23 PM, Robert Hanson wrote:
I'm wondering if we should try to produce a really
Dear Eric,
Sorry to know that the Java problem started to affect also users from OSX older
than 10.7
I'm running 10.7 and have several problems: Jmol applet from a server always
requests authorization (it seems to forget preferences), and I'm having
problems running Jmol applet on local web
How do I know which version of JSmol I have running on a page?
How do I know which rendering engine (Java, WebGL, HTML5) is in use?
Thank you in advance,
Jaim
--
Everyone hates slow websites. So do we.
Make your web
Dear Jmol,
The following script from JSmol/Jmol button frame 4 8; delay 0.5;frame play
plays great, but, the first step is to draw frames 4 to 8 all together, then it
starts playing. This happens both on Jmol and JSmol.
Is this the expected behavior? How may I construct a button to play a
Thank you for a prompt reply. It works great by adding the RANGE word.
On Mar 14, 2013, at 6:29 PM, Rolf Huehne wrote:
On 03/14/2013 05:13 PM, Jaime Prilusky wrote:
Dear Jmol,
The following script from JSmol/Jmol button frame 4 8; delay 0.5;frame play
plays great, but, the first step
Clean drawing. Fast. Very nice!.
I would add labels, or the option to label atoms. You will need them for
teaching.
Jaim
On Mar 24, 2013, at 8:19 PM, Robert Hanson wrote:
OK, here's a first shot:
http://chemapps.stolaf.edu/jmol/jsmol/lite.htm
Tell me what you think.
Subtracting 2 seconds off
when done.
Packaging everything and releasing a JSmol/Jmol extension for Mediawiki is on
my list of tasks, although I've been busy on other Jmol related task.
Jaim
--
Dr Jaime Prilusky
Head Bioinformatics
RD Bioinformatics and Data Management
Department of Biological Services
Weizmann Institute
is an important issue to cope with if you want a slight
chance of seeing Jmol used.
Nico
[1] http://www.mediawiki.org/wiki/Amsterdam_Hackathon_2013
On Tue, Apr 23, 2013 at 5:36 PM, Jaime Prilusky
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
Hi Nico,
It's good
Very nice!!
Jaim
__
Dr Jaime Prilusky
Head Bioinformatics
RD Bioinformatics and Data Management
Department of Biological Services
Weizmann Institute of Science
76100 Rehovot - Israel
mail: jaime.prilu...@weizmann.ac.il
tel: 972-8-9344959
fax: 972-8-9344113
OCA, http://oca.weizmann.ac.il
On Jul 24, 2013, at 2:47 PM, Robert Hanson wrote:
OK, this is fixed.
http://chemapps.stolaf.edu/jmol-13.3.3_2013.07.24.zip
No visible side effects at http://ispcsrv.weizmann.ac.il/a2jmolb/browse
Jaim
--
See everything
Is there a way to set an arbitrary string for each atom to be displayed when
hovering the atom? A real arbitrary string, not composed out of atom number,
element, etc?
Jaim
--
Learn the latest--Visual Studio 2012,
Hola Angel,
Thank you for a prompt reply.
I was looking for an extension of the following way of setting properties for
individual atoms. Besides spacefill and color, I would like to have an
individual hover arbitrary string for each atom.
select atomno=11; spacefill 4.00; color [xFF66FF]
This looks interesting.
Thank you again,
Jaim
On Sep 1, 2013, at 1:06 PM, Angel Herráez angel.herr...@uah.es
wrote:
I found that hover can reflect the label text, and label can indeed be
assigned per atom.
So, as long as you don't need to use labels, this seems to do the trick:
hover
Is this structure not longer valid? We have several scripts using it in the
past and things were Ok.
Today, running on Jmol 13.0.1 it returns parsing error. Does it works Ok on
previous versions of Jmol? On newer versions?
Jaim
data connect;
connect_atoms
91 198040960.4
calculated for this bond (only relevant for hydrogen bonds)
6 is the human-readable meaning of the coded bond type (ignored)
Bob
On Mon, Sep 16, 2013 at 1:45 PM, Jaime Prilusky
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
Is this structure not longer valid? We have several
Add php to the file location. Change the path to /jmol/jsmol/php/jsmol.php
Jaim
On Sep 17, 2013, at 1:57 PM, björn bjoern-oliver.goh...@charite.de
wrote:
Hello,
i use jsmol on my website.
Everthing works fine but i cannot download the view anymore (as png or jsmol).
I changed nothing.
Art,
Have you considered http://proteopedia.org ?
Jaim
On Sep 18, 2013, at 12:42 AM, Cox, Arthur G. wrote:
I'd like to publish a few web pages with Jmol applets, but don't necessarily
want to use my own computer.
Does anyone have a recommendation for a hosting company that supports java
I'm currently improving and simplifying the JSmolExtension for MediaWiki I
developed and currently using in Proteopedia.org.
Hope to release the new version next week. Please be patient.
Regards,
Jaim
__
Dr Jaime Prilusky
Head Bioinformatics
RD Bioinformatics and Data Management
Department
Excellent. Will this also be true for the applet version?
In one year from now we’ll see if Java's still required, and, if the renewal
requires a payment, find sources for that.
Jaim
__
Dr Jaime Prilusky
Head Bioinformatics
RD Bioinformatics and Data Management
Department of Biological Services
Thank you for this release. Runs Ok on Mac 10.9 FFox 25.0.1
Unable to convince Safari 7.0 to run a local applet.
Also tried with a Proteopedia exported page and (again FFox on Mac) it works
great!!
Jaim
On Nov 24, 2013, at 8:47 AM, Robert Hanson
hans...@stolaf.edumailto:hans...@stolaf.edu
The “Bond/BondSet.js” error appears also on Mac Firefox 25.0.1, but the applet
continues working. You may see error reports with Firebug.
This might come from lines like this one in Bond.js and other files:
J/modelset/Bond.js:Clazz.superConstructor (this, J.modelset.Bond.BondSet, []);
The call
On Nov 27, 2013, at 12:30 AM, Robert Hanson hans...@stolaf.edu wrote:
Yes, it's related to the fact that BondSet is an inner class of Bond.
Something is as happening out of order. Utlimately, Bond.BondSet is created
just fine. Very curious!
Found in your code a few other calls to
Rolf,
Maybe the way I work on Proteopedia might help you.
I have a CGI script that sends the content of the structure files to
Jmol/JSmol: getlateststructure
The script gets as a parameter the name of the file to return or the PDB id for
that file, and looks for the ending “.gz” on that
/Teaching_Strategies_Using_Proteopedia
Please feel free to write if you have questions or need any help.
Regards,
Jaim
__
Dr Jaime Prilusky
Head Bioinformatics
RD Bioinformatics and Data Management
Department of Biological Services
Weizmann Institute of Science
76100 Rehovot - Israel
mail: jaime.prilu...@weizmann.ac.il
On Dec 12, 2013, at 6:19 PM, Robert Hanson hans...@stolaf.edu wrote:
It's still there. Should work. RCSB uses this. Proteopedia, I think.
On Proteopedia we use MobileDetect.php ( http://mobiledetect.net ) to send back
to the user a proper configuration based on the platform.
It seems that
What's the correct syntax to get from JSmol applet the isosurface data as JVXL
string in javascript?
I guess that some variation of Jmol.getPropertyAsJavaObject(jmolApplet0,
isosurfaceData) could do.
Thank you in advance,
Happy Holidays,
Jaim
What's the correct syntax to get from JSmol applet the isosurface data as JVXL
string in javascript?
I guess that some variation of Jmol.getPropertyAsJavaObject(jmolApplet0,
isosurfaceData) could do.
Thank you in advance,
Happy Holidays,
Jaim
, you could use:
var xmlData = Jmol.evaluate(jmolApplet0, script('show isosurface'))
On Sat, Dec 28, 2013 at 1:31 PM, Jaime Prilusky
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
What's the correct syntax to get from JSmol applet the isosurface data as JVXL
string
;
isosurface solvent;
show isosurface;
Jaim
__
Dr Jaime Prilusky
Head Bioinformatics
RD Bioinformatics and Data Management
Department of Biological Services
Weizmann Institute of Science
76100 Rehovot - Israel
mail: jaime.prilu...@weizmann.ac.il
tel: 972-8-9344959
fax: 972-8-9344113
OCA, http
Jmol 14.0.3 shows misplaced elements when requesting rockets representation on
3STU
Try the following, on either Jmol.jar or JmolApplet:
file - get PDB - 3STU
Select - All
Style - Structures - Rockets
Jmol version 13.2.8 renders Ok.
Jmol 14.0.3 shows misplaced elements.
Jaim
https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.0/Version%2014.0.4
Not much here, but one important fix for ribbons, so if you do anything with
proteins be sure to download this modification in 14.0 and 14.1.
Bob
Thank you.
Fixed the misplaced rockets elements.
PSE conversion
Are you in any way disabling or capturing events from mouse right-click ?
Jaim
On Jan 7, 2014, at 5:56 PM, Eric Martz ema...@microbio.umass.edu wrote:
I cannot seem to get the JSmol menu to open in 14.0.3 e.g.
http://firstglance.jmol.org/fg.htm?mol=1d66use=html5
Any suggestions?
Eric
We used to have a call to javascript as part of the script text, but that is
not longer working:
Jmol.script(jmol0,'load data/123.pdb; javascript alert(“Back”);’);
On the following example, the alert() happens before the script gets executed.
The threading mechanism plays here against us.
It would be good for set platformSpeed to apply also when zooming in or out the
model.
It does work as advertised on rotation.
Jaim
--
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On 14.0.5 , rendering with HTML5, set platformSpeed works perfect when the
zooming action is driven by shift-cursor up/down.
It does not work when zooming with the mouse wheel.
Jaim
--
CenturyLink Cloud: The Leader in
is
the same for both Java and HTML5 modes.
Bob
On Mon, Jan 13, 2014 at 5:12 AM, Jaime Prilusky
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
We used to have a call to javascript as part of the script text, but that is
not longer working:
Jmol.script(jmol0,'load data/123
Even if adding refresh to Jmol.script, the alert happens before the model gets
loaded:
Jmol.script(jmol0,'load data/123.pdb; select all; color blue; refresh;');
alert(“Back”);
Jaim
On Jan 13, 2014, at 2:03 PM, Angel Herráez angel.herr...@uah.es wrote:
I agree that the use of refresh is often
Have you tried it on 14.0.5 with HTML5?
Jaim
On Jan 13, 2014, at 2:26 PM, Otis Rothenberger
osrot...@chemagic.commailto:osrot...@chemagic.com wrote:
I use the javascript command frequently. From past experience, arguments in
functions can cause issues. At a minimum, I would put quotes around
?
Just curious.
Jaim
On Mon, Jan 13, 2014 at 7:02 AM, Jaime Prilusky
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
On 14.0.5 , rendering with HTML5, set platformSpeed works perfect when the
zooming action is driven by shift-cursor up/down.
It does not work when zooming
initial way
is correct; just add a REFRESH command prior to that if you want the model to
be displayed during the alert.
On Mon, Jan 13, 2014 at 6:21 AM, Jaime Prilusky
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
Even if adding refresh to Jmol.script, the alert
Thank you for a prompt reply, but it’s not working for me on 14.0.5.
The command waitmessage is undocumented. Maybe it’s something you added?
On Jan 15, 2014, at 1:48 PM, Rolf Huehne rhue...@fli-leibniz.de wrote:
On 01/15/2014 12:18 PM, Jaime Prilusky wrote:
I would like to have a message
Please disregard previous mail. Your suggestion of using waitmessage works
perfect.
Thank you again,
Jaim
On Jan 15, 2014, at 3:06 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.il
wrote:
Thank you for a prompt reply, but it’s not working for me on 14.0.5.
The command waitmessage
that there is no
updating it, because the calculation is not interruptable at all, including
updating any such message.
On Wed, Jan 15, 2014 at 6:18 AM, Jaime Prilusky
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
I would like to have a message “Working …” while Jmol
Rolf: Thank you for testing on other browsers and platforms. While developing I
stay on Mac.
Bob: I hope that this detailed report might help you find a solution for the
problem.
Jaim
On Jan 16, 2014, at 8:14 PM, Rolf Huehne rhue...@fli-leibniz.de wrote:
On 01/16/2014 06:14 PM, Jaime
...@stolaf.edumailto:hans...@stolaf.edu wrote:
Yes, I think I found it. delay 0.01 should work even though refresh does not:
set echo top left
echo working...
delay 0.01
echo
Please try that; I'll also get refresh working. Testing now.
On Thu, Jan 16, 2014 at 1:27 PM, Jaime Prilusky
jaime.prilu
Dear Bob,
On Safari Mac, with jsmol 14.1.6_dev_2014.01.16 , the notice while working
performs great with delay 0.1 instead of refresh
Thank you for the suggestion.
Jaim
On Jan 16, 2014, at 10:10 PM, Jaime Prilusky
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
Thank
down: echo/surface test. I'm guessing the flash is the
calculation. everything before that is file loading.
Bob
On Thu, Jan 16, 2014 at 3:10 PM, Jaime Prilusky
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
Thank you for the new version.
I would say that now
getProperty ligandInfo returns a nice list of elements in the HET record of the
PDB file, with some exceptions, like ATP and ADP.
Those are not included in the ligandInfo report. Tested on Jmol 14.0.7 (both
Java and HTML5) on several structures, including 1s22 and 1php
Is there other
Thank you Angel for the explanation. Still looking for a solution.
Jaim
On Jan 22, 2014, at 5:00 PM, Angel Herráez angel.herr...@uah.es wrote:
I'm guessing, but ATP may be recognized as nucleic by Jmol
algorithm and hence excluded from the ligand set, which is not
protein, not nucleic, not
?
On Wed, Jan 22, 2014 at 12:16 PM, Jaime Prilusky
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
Thank you Angel for the explanation. Still looking for a solution.
Jaim
On Jan 22, 2014, at 5:00 PM, Angel Herráez
angel.herr...@uah.esmailto:angel.herr...@uah.es wrote
Is there a way to force loading JSmol when loading/rendering a page? JQuery
should be able to do this.
This is why we might need to start with a fresh loaded JSmol: When clicking a
‘back to previous page’ button on On Mac 10.9.1, Safari 7.0.1, JSmol renders
non-operational. On Firefox 26.0,
, Jaime Prilusky
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
Is there a way to force loading JSmol when loading/rendering a page? JQuery
should be able to do this.
This is why we might need to start with a fresh loaded JSmol: When clicking a
‘back to previous page
onload=
2) JSmol ready function
3) JSmol structure loaded callback
Maybe also, server setting related to caching???
Otis
--
Otis Rothenberger
o...@chemagic.commailto:o...@chemagic.com
http://chemagic.com
On Jan 30, 2014, at 11:57 AM, Jaime Prilusky
jaime.prilu
On Mac 10.9.2, both Safari and Firefox 28.0, JSmol fails with message:
TypeError: 'undefined' is not an object (evaluating
'this.stm.jmolStatusListener.isStereoSlave')
JSmol loads, able to open popup menu, no frank.
Java version, Jmol_S, works Ok.
Jaim
On Mar 22, 2014, at 2:05 AM, Robert
chemapps.stolaf.edu/jmol/zip/jmol-14.1.12_2014.03.22.zip
On Mar 23, 2014, at 6:55 PM, Eric Martz ema...@microbio.umass.edu wrote:
I am getting file not found for the URL below.
Someone please tell me where to get the current 14.1.12 -- thanks! Eric
At 3/23/14, Robert Hanson wrote:
On Apr 26, 2014, at 6:58 AM, Robert Hanson
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:
http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.1/Jmol%2014.1.14/
Was the release 14.1.14 removed from sourceforge.nethttp://sourceforge.net?
The latest version I’m able to access is
is available on WebGL at this
time.
Jaim
--
Dr Jaime Prilusky
Head Bioinformatics
RD Bioinformatics and Data Management
Department of Biological Services
Weizmann Institute of Science
76100 Rehovot - Israel
eml: jaime.prilu...@weizmann.ac.il
fax: 972-8-9344113
tel: 972-8-9344959
OCA, http
with other PDB ids.
Suggestions?
Thanks in advance,
Jaim
--
Dr Jaime Prilusky | [EMAIL PROTECTED]
RD Bioinformatics and Data Management |
Weizmann Institute of Science | fax: 972-8-9344113
76100 Rehovot - Israel | tel: 972-8-9344959
info URL
through green)..
Jaim
--
Dr Jaime Prilusky | [EMAIL PROTECTED]
RD Bioinformatics and Data Management |
Weizmann Institute of Science | fax: 972-8-9344113
76100 Rehovot - Israel | tel: 972-8-9344959
info URL http://bip.weizmann.ac.il/staff
Jaime Prilusky | [EMAIL PROTECTED]
RD Bioinformatics and Data Management |
Weizmann Institute of Science | fax: 972-8-9344113
76100 Rehovot - Israel | tel: 972-8-9344959
info URL http://bip.weizmann.ac.il/staff/jaime_prilusky.html
OCA is at http
) and it's
possible to access Jmol applet functions with the pulldown menu.
The browser crashes instantly when executing any Jmol.js call.
Normal javascript calls, like the button bellow, works fine.
input type=button value=back onClick=javascript:history.go(-1);
Jaim
--
Dr Jaime Prilusky
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