That is really a good catch! I found it. It has to do with an attempt I
made to make JSmol totally asynchronous. The problem occurs if, in the
initiation of the minimization after loading, it is discovered that a file
is needed. JSmol would then have to go back and save its processing state,
get t
Paul,
The thing that surprised me was that the model loaded! I didn't know you could
use a molfile in a data load. I guess because the original example in the docs
used a XYZ file, I got in my head that you had to use an XYZ file with a data
load.
I avoided using the "W" word in my note, but n
Well, it did work… 3 years ago…
I’ve implemented this in a previous page that I haven’t touched for a while.
The migration to HTML5 is now overdue and I wanted to update to the latest
version (and take profit of the speed bump in JS execution).
The workaround you are suggesting indeed works, but
Hi Paul,
I played with this for a while. Did Filter “2d” ever work with load data? I
keep getting jmol script errors if I try to incorporate the filter. I tried
several locations for insertion.
This alternative gets the job done:
load DATA "model"
Ethane
http://www.ichemlabs.com
2 1 0 0
Hi Jmolers,
I’ve tried with the 2 latest versions of Jmol (14.3.16, 14.2.15) and they both
seem broken in respect with this command.
Test case :
copy and paste the following in Jmol console :
load DATA "model"
Ethane
http://www.ichemlabs.com
2 1 0 0 0 0999 v2000
-0.4330
Thanks, Rolf. The trick was to carry over the key modifications in the drag
operation from what was down when the mouse was pressed. I did have a note
to myself indicating that Mac OS (and I guess also Linux) are different
from Windows in that regard, failing to indicate the actual key status in
th
On 09/05/2015 06:44 AM, Robert Hanson wrote:
> This one is for Rolf. Please check
>
> -- Don't Work (as expected) -
> SHIFT+RIGHT+drag_rotateZrotate Z
> -> '_rotateZorZoom' instead of 'rotate Z'
>
> MIDDLE+drag _rotateZorZoom rotate Z (h
This one is for Rolf. Please check
-- Don't Work (as expected) -
SHIFT+RIGHT+drag_rotateZrotate Z
-> '_rotateZorZoom' instead of 'rotate Z'
MIDDLE+drag _rotateZorZoom rotate Z (horizontal motion of mouse) or
zoom (vertical motion of mou
It's a bug. The MOVE command does do different things than the MOVETO
command; the idea is that for general work MOVETO is more capable, but the
effects are definitely different.
On Tue, Sep 1, 2015 at 8:36 AM, Rolf Huehne wrote:
> On 08/25/2015 04:28 PM, Robert Hanson wrote:
> > OK, let's try a
On 09/01/2015 03:36 PM, Rolf Huehne wrote:
> On 08/25/2015 04:28 PM, Robert Hanson wrote:
>> OK, let's try again, please. I really appreciate all this testing. Rolf, I
>> am especially interested in if this fixes your JenaLib startup problem.
>>
> The 'move' command doesn't do anything if the time
On 08/25/2015 04:28 PM, Robert Hanson wrote:
> OK, let's try again, please. I really appreciate all this testing. Rolf, I
> am especially interested in if this fixes your JenaLib startup problem.
>
The 'move' command doesn't do anything if the time is set to zero, e.g.:
move 180 0 0 0 0 0 0 0 0;
thanks -- taken care of.
On Mon, Aug 31, 2015 at 8:57 AM, Ron Mignery wrote:
> "plot properties" without parameters (I know - user error) now freezes the
> Jmol application.
> then:
> $ print _version
> 1402015
> $ plot properties
> script ERROR: invalid argument
>
> plot property
"plot properties" without parameters (I know - user error) now freezes the
Jmol application.
then:
$ print _version
1402015
$ plot properties
script ERROR: invalid argument
plot property <<
$
now:
$ print _version
1403016
$ plot properties
$ !exit
script execution halted with !exit
$
On 08/29/2015 12:02 AM, Robert Hanson wrote:
> Go to http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
>
> In the search box, enter
>
>! set debug
>
> do your mouse/key actions
>
> then click on the "show" link under the applet next to "info"
>
The messages are identical in Firefox and Chromium a
Go to http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
In the search box, enter
! set debug
do your mouse/key actions
then click on the "show" link under the applet next to "info"
I see:
Script completed
Jmol script terminated
script 2 started
logging level set to 5
logLevel = 5
Script compl
On 08/28/2015 05:32 PM, Robert Hanson wrote:
> Please use
>
> set debug
>
> then do your tests and see what is reported. Jmol will report the
> key-mouse combination such as:
>
>
> LEFT+down
> LEFT+up
> SHIFT+RIGHT+down
> SHIFT+RIGHT+up
>
> and let me know what it gives.
>
I can't see any messages
Please use
set debug
then do your tests and see what is reported. Jmol will report the
key-mouse combination such as:
LEFT+down
LEFT+up
SHIFT+RIGHT+down
SHIFT+RIGHT+up
and let me know what it gives.
Bob
--
See also my message subject
Mouse gestures fail in OS X Firefox Java
(Aug 22)
-Eric
On 8/27/15 7:25 AM, Rolf Huehne wrote:
> On 08/25/2015 04:28 PM, Robert Hanson wrote:
>> OK, let's try again, please. I really appreciate all this testing. Rolf, I
>> am especially interested in if this fixes your
On 08/25/2015 04:28 PM, Robert Hanson wrote:
> OK, let's try again, please. I really appreciate all this testing. Rolf, I
> am especially interested in if this fixes your JenaLib startup problem.
>
> http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.16/Jmol-14.3.16_2015.0
OK
I should have mentioned that the page works just fine.
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
> On Aug 26, 2015, at 10:36 AM, Robert Hanson wrote:
>
> OK, thanks, Otis. All of those are just standard warnings, not errors.
>
> --
OK, thanks, Otis. All of those are just standard warnings, not errors.
--
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Bob,
I cleaned my FF problem out so that there would not be any confusion. My issue
was related to a known FF bug with document.execCommand. Easy solution was to
opt FF out on the commands that were related to object resizing. This was not a
Local Storage issue as I originally thought.
With th
Ah! I know what that is
On Tue, Aug 25, 2015 at 1:29 PM, Paul PILLOT wrote:
> I have also encountered a problem with the shorthand / in fractional
> coordinates :
> draw pl1 plane {0 0 0/} {1 0 0/} {1/2 1 0/};
> doesn’t work : Erreur du compilateur de script: spécification de modèle
> incorr
Good catch Rolf !
Indeed, setting the browser language to english disables these error messages
AND allows for context menu display.
Paul
> Le 25-08-2015 à 15:24, Rolf Huehne a écrit :
>
> Am 25.08.15 um 20:59 schrieb Philip Bays:
>> Do these errors only show up on your web page, or do they sho
Paul and Bob,
Chrome appears OK for me. Firefox is whining about a whole mess of syntax
errors in various Jmol .js files. I must admit that FF is becoming a real pain
for me. I haven’t checked for a while. I see it’s having problems with my Local
Storage error catching, but that’s unrelated to
Am 25.08.15 um 20:59 schrieb Philip Bays:
> Do these errors only show up on your web page, or do they show up using some
> of Bob’s sample pages? I have the newest on both a local server and on the
> campus server, but not integrated into my web pages yet. But I can access
> one of Bob's sampl
Do these errors only show up on your web page, or do they show up using some of
Bob’s sample pages? I have the newest on both a local server and on the campus
server, but not integrated into my web pages yet. But I can access one of
Bob's samples from that server to see what happens. I am run
Thanks Otis,
I am also running pages from my local web server (localhost). I haven’t spotted
the setting you are referring to.
I have made further tests with firefox 40 and Chrome 44.
The three browsers give the same consistent error messages (that don’t prevent
jsmol from working).
Paul
> Le
I do see this draw error - wasn’t familiar with the shorthand notation.
Non-shorthand notation seems to work for me OK.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
> On Aug 25, 2015, at 2:29 PM, Paul PILLOT wrote:
>
> I have also encountered a problem with the shorthand / i
Bob and Paul,
I’m not seeing this (below) in MacOS X 10.10.4 (Yosemite) and Safari 8.0.7.
I should mention that I’m running locally with internet connection - i.e. all
my AJAX remote calls working.
This means that I run Safari with “Disable Local File Restrictions” checked.
Otis
--
Otis Rothe
I have also encountered a problem with the shorthand / in fractional
coordinates :
draw pl1 plane {0 0 0/} {1 0 0/} {1/2 1 0/};
doesn’t work : Erreur du compilateur de script: spécification de modèle
incorrecte
draw pl1 plane {0 0 0/} {1 0 0/} {1/2 1 0/}
whereas the following
Hi Bob,
the 2 error messages on startup are displayed on MacOS X.10.5, Safari 8.0.8
TypeError: undefined is not an object (evaluating
'J.api.Interface.getInterface') try/catch path:
0 function (b, d)
args[0]=TypeError: undefined is not an object (evaluating 'J.api.Int...
args[1]=function () {a
On 08/25/2015 04:28 PM, Robert Hanson wrote:
> OK, let's try again, please. I really appreciate all this testing. Rolf, I
> am especially interested in if this fixes your JenaLib startup problem.
>
> http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.16/Jmol-14.3.16_2015.0
Bob,
Both my problems are fixed. I’ll continue working with it during the course of
the day as I continue to clean up my JavaScript and server scripts.
By the way, this is the new model kit - not yet running new JSmol:
http://chemagic.com/molecules/VMKMINInotes.htm
It makes extensive use of Lo
OK, let's try again, please. I really appreciate all this testing. Rolf, I
am especially interested in if this fixes your JenaLib startup problem.
Bob
http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.16/Jmol-14.3.16_2015.08.25-binary.zip/download
--
Rolf, the issue is the move commands at the end of your start-up script. I
can duplicate the lock-up problem on Windows with that, so I should be able
to figure out what is going on there.
Bob
--
OK, sounds like I need to sit down at a Mac and see what is happening.
Could be those recent mouse wheel aliases I set up. Will do. Thanks, Rolf.
On Mon, Aug 24, 2015 at 5:31 AM, Rolf Huehne wrote:
>
> I tested version 14.3.16_2015.08.21 with the 'Jena3D Viewer' HTML5
> (
> http://jenalib.fli-l
Yes, and a few other issues with that. OK, that is FINALLY fixed
On Mon, Aug 24, 2015 at 8:09 AM, Rolf Huehne wrote:
> On 08/18/2015 07:06 AM, Robert Hanson wrote:
> >
> http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.16/
> >
> > Now holds the latest test build t
On 08/18/2015 07:06 AM, Robert Hanson wrote:
> http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.16/
>
> Now holds the latest test build that I hope will lead to Jmol 14.4.0
> release later this week or next.
>
> I would it if you would test it if you have a site and have
Am 18.08.15 um 07:06 schrieb Robert Hanson:
> http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.16/
>
> Now holds the latest test build that I hope will lead to Jmol 14.4.0
> release later this week or next.
>
> I would it if you would test it if you have a site and have
Dear Bob,
I have tested the Aug 21 Jmol in FirstGlance and the only issue I
spotted was the one about fragmentary residues (already reported in a
separate email).
So it passed with flying colors! Bravo!!!
Eric
--
On 08/19/2015 04:12 PM, Robert Hanson wrote:
> I do not understand why sometimes the build Jmol.jar does not match what I
> have when debugging. But that was the culprit with Rolf's problem.
>
> http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.16/Jmol-14.3.16_2015.08.19
Thank you.
This new version fixed the "Errors on missing Isosurface file":
electrostatics2, 3BSN_3BSO, hupa_LC, HupA_2 and HupA_3
The rest stays:
The error of PyMOL reader not reading "H69" as "helix"
(RGS-Ga_8pdb_structures_aligned_S90_20.5.15.pse) persists. The generated JPNGJ
contains two
I do not understand why sometimes the build Jmol.jar does not match what I
have when debugging. But that was the culprit with Rolf's problem.
http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.16/Jmol-14.3.16_2015.08.19-binary.zip/download
Jmol.___JmolVersion="14.3.16_2
round two: Just PyMOL reader issues, I think.
http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.16/Jmol-14.3.16_2015.08.18-binary.zip/download
Rolf, please try this one and send me spt files that fail to run. I still
cannot reproduce your %% error. I was sure I had fix
Rolf, could you send me an spt file? I cannot reproduce these problems.
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MUCH appreciated, Rolf! I will work on this tonight and have another upload
ready for you soon.
--
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On 08/18/2015 07:06 AM, Robert Hanson wrote:
> http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.16/
>
> Now holds the latest test build that I hope will lead to Jmol 14.4.0
> release later this week or next.
>
> I would it if you would test it if you have a site and have
http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.16/
Now holds the latest test build that I hope will lead to Jmol 14.4.0
release later this week or next.
I would it if you would test it if you have a site and have the time to do
that.
Up-to-date documentation can be
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