Eric, there is a way around this, but I have to check to see if there is a
bug there. The issue is that the zoom command also recenters. The solution
is to do the moveto command with the same orientation:
var q = script(show orientation rotation)
moveto quaternion @{!q} 100 0 10
That sets the
no bug -- that's the way it should work. The command is:
moveto quaternion @{!script(show orientation rotation)} 100 0 10
We could talk about making that easier to code.
On Mon, Nov 9, 2009 at 6:38 PM, Robert Hanson hans...@stolaf.edu wrote:
Eric, there is a way around this, but I have
Eric,
print getProperty(orientationInfo.zoom)
See also
print getProperty(orientationInfo)
So, for example, you could divide the zoom in half and not change anything
else by:
var x = getProperty(orientationInfo.moveto).split( )
x[8] = x[8]/2
script inline @{x.join( )}
// get an array of all
On Tue, Nov 10, 2009 at 5:47 AM, Brian McMahon b...@iucr.org wrote:
Earlier this year Bob introduced very nice functionality to move a
label dynamically by SHIFT-click (application) or CTRL-click (applet)
It's the same code -- should be the same key-combination. -- SHIFT, not
CTRL
on an
-0600, Robert Hanson wrote:
On Tue, Nov 10, 2009 at 5:47 AM, Brian McMahon b...@iucr.org wrote:
Earlier this year Bob introduced very nice functionality to move a
label dynamically by SHIFT-click (application) or CTRL-click (applet)
It's the same code -- should be the same key
it's not quite ready to go out, Eric.
On Tue, Nov 10, 2009 at 9:52 AM, Eric Martz ema...@microbio.umass.eduwrote:
Dear Bob and Egon,
We would like to upgrade Proteopedia to 11.8.9. The failure to start
animation automatically bug that Bob fixed for 11.8.9 is the last
one we know about that
holy cow, it actually loaded.
On Tue, Nov 10, 2009 at 1:15 PM, Egon Willighagen
egon.willigha...@gmail.com wrote:
Thanx, Henry!
http://www.nature.com/nchem/journal/v1/n7/media/nchem.373_jmol.html
Egon
--
Post-doc @ Uppsala University
Homepage: http://egonw.github.com/
Blog:
yes, lots of spaces will do it.
On Sun, Nov 8, 2009 at 12:12 PM, Eric Martz ema...@microbio.umass.eduwrote:
I am placing a banner of text across the top of Jmol like this:
http://www.umass.edu/molvis/tests/banner.html
(Jmol's background is black; the echo has a white background with black
version=11.9.8
# new feature: labels HIDE and labels DISPLAY do exactly that
select oxygen
labels HIDE
select carbon
labels DISPLAY
On Tue, Nov 10, 2009 at 10:09 AM, Robert Hanson hans...@stolaf.edu wrote:
This is fixed for Jmol 11.9.8 and Jmol 11.8.9.
select [someAtoms]
set
whatever, but I didn't fix that. It's the same.
Well, in Jmol 11.8.8 set windowcentered
false did NOT free zoom from recentering in the window center, but I
see that this is fixed in 11.8.9 -- HOORAY! So now set
windowcentered false is the equivalent of Chime's set zoomcenter
off which
For zoomto, this is fixed for Jmol 11.8.10 and 11.9.9. It should not be
doing any reorienting at all. Moveto, on the other hand, must do that.
On Wed, Nov 11, 2009 at 7:30 PM, Eric Martz ema...@microbio.umass.eduwrote:
Thanks to everyone who helped to release 11.8.9. Its great!
Bob, in
-- no
relation to the windowCentered parameter.
moveto /* time, axisAngle */ 10.0 {0 0 0 0} /* zoom, translation */ 150.0
30.0 30.0
Bob
On Thu, Nov 12, 2009 at 7:07 AM, Robert Hanson hans...@stolaf.edu wrote:
For zoomto, this is fixed for Jmol 11.8.10 and 11.9.9. It should not be
doing any
Let us know how that works with Sun Java. I'm not seeing any problem. But I
do note that by using the applet tag you are not properly registering the
applets within the JmolAppletRegistry, which allows communication among
applets. Please see if the problem persists while using Jmol.js. If you want
I can't reproduce the problem with zoom after translate. Works for me --
stays not windowcentered.
reset should reset the windowCentered flag. If you don't want it to, use
reset;set windowcentered false
Bob
On Sun, Nov 15, 2009 at 11:49 AM, Eric Martz ema...@microbio.umass.eduwrote:
Dear
my pleasure.
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
On Mon, Nov 16, 2009 at 7:01 AM, Rzepa, Henry h.rz...@imperial.ac.ukwrote:
Henry, not a problem. Just another day in the life of a hacker. ;)
More for the hacker Bob
The following
script
Jmol users,
Jmol 11.9.9 will have a couple of mouse-related new features. One that
should be useful is
show mouse
or
show mouse [keyword]
such as
show mouse move
or
show mouse pick
These return information about what the mouse buttons do.
In addition, because underneath the surface Jmol
Thanks, Rolf. Quite possible about the wheel -- I didn't test this.
swipe -- I probably didn't explain that correctly.
On Wed, Nov 18, 2009 at 7:13 AM, Rolf Huehne rhue...@fli-leibniz.de wrote:
swipe -- with a finger this is a rapid movement that releases as it
terminates. With a mouse,
: Tue, 17 Nov 2009 17:49:40 -0600
From: Robert Hanson hans...@stolaf.edu
Subject: [Jmol-users] feedback appreciated
To: jmol-users@lists.sourceforge.net
Message-ID:
ba9c0bd60911171549t5723db22w38f76ec64ddec...@mail.gmail.com
Content-Type: text/plain; charset=iso-8859-1
Jmol users,
Jmol
OK, please take another look at
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
I think I fixed the right-side zoom business, and because I thought was
working so well, I opted to leave it in as default Jmol, not a special
action. The cursor changes to a vertical zoom cursor when you move
maybe the bottom 2%?
2009/11/18 Angel Herráez angel.herr...@uah.es
On 18 Nov 2009 at 13:17, Robert Hanson wrote:
OK, please take another look at
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
Nice!
This brings an idea: how about having also the 6% top of the applet do
Z
Why not just make it anywhere you want? any function?
On Wed, Nov 18, 2009 at 5:12 PM, Egon Willighagen
egon.willigha...@gmail.com wrote:
On Wed, Nov 18, 2009 at 10:38 PM, Jeff Hansen jhan...@depauw.edu wrote:
Lets just go extreme with this. Make every side of the applet available
for
Hmm, I was thinking more along the lines of within a certain area of the
window. You can always trap a pickCallback for atoms.
On Wed, Nov 18, 2009 at 5:19 PM, Egon Willighagen
egon.willigha...@gmail.com wrote:
On Thu, Nov 19, 2009 at 12:14 AM, Robert Hanson hans...@stolaf.edu
wrote:
Why
function testit {
print _atomPicked
}
set pickCallback jmolscript:testit;
On Wed, Nov 18, 2009 at 5:29 PM, Egon Willighagen
egon.willigha...@gmail.com wrote:
On Thu, Nov 19, 2009 at 12:27 AM, Robert Hanson hans...@stolaf.edu
wrote:
Hmm, I was thinking more along the lines
comes on --- when the display
is re-awakened, the display is static. Not an issue, as far as I am
concerned, but I thought it fell into the realm of unexpected.
-Tom
PS -- Firefox 3.0.14 under RHEL5 (32bit on a 64bit machine)
On Wed, Nov 18, 2009 at 11:17 AM, Robert Hanson hans
Just about to release 11.9.9, but I thought it would be good to pass this
idea past jmol-users.
The idea involves two new commands:
bind
unbind
These command can be used to tie mouse actions to Jmol actions or
user-defined scripts. In addition, to check current bindings, you can use
getproperty
forgot to point out that this is all testable at
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
On Thu, Nov 19, 2009 at 5:44 PM, Robert Hanson hans...@stolaf.edu wrote:
Just about to release 11.9.9, but I thought it would be good to pass this
idea past jmol-users.
The idea involves
Jmol is GPLP, not GPL. So we don't care how you use the applet provided any
modifications you make to the code you make public and not LESS restricted
than GPLP. If I have this correct, and I'm not sure I do, then you are OK
there.
What we have to be careful with Jmol to do is not incorporate any
Jan, this has nothing to do with Jmol.js. It's a change in the versions of
Jmol. I try to minimize that, but I think in the case of contourlines we may
have a backward-compatibility issue. First upgrade to the latest 11.8, and I
would appreciate your checking 11.9 as well. These are pretty recent
Andy, welcome to Jmol. You are going to find it exceptionally easy to do all
the things you suggest.
On Sun, Nov 22, 2009 at 7:15 PM, Andy Lu andylu0...@gmail.com wrote:
I just started programming with JMol java files and I got the
Integration.java file to work from JMol website.
I have 5
effect, despite repeated reloads of the page?? Very strange!
Anyway, thank you for the replies.
Jan
Robert Hanson hans...@stolaf.edu skrev:
Jan, this has nothing to do with Jmol.js. It's a change in the versions
of
Jmol. I try to minimize that, but I think in the case of contourlines we
may
not sure where
to start.
Thank you for your explanation!
On Mon, Nov 23, 2009 at 7:50 AM, Robert Hanson hans...@stolaf.edu wrote:
Andy, welcome to Jmol. You are going to find it exceptionally easy to do
all the things you suggest.
On Sun, Nov 22, 2009 at 7:15 PM, Andy Lu andylu0...@gmail.com wrote
;);
viewer.evalString(drawHover on;);
I am not sure how to set those values. I am sensing I am missing something
in front of quotes. Thanks once again!
On Mon, Nov 23, 2009 at 11:17 PM, Robert Hanson hans...@stolaf.eduwrote:
OK, so there are two things here: JavaScript and Jmol scripts
When an applet has sync on, then it receives messages from any other applet
on its synchronization set. By default, this set is all the applets on its
page. But you can be more specific than that by using
jmolSetSyncId(n)
where n is some number. So set n to one number just before the
On the command line of the applet (the URL line of the browser) you can add
?JMOLJAR=...
and then that will allow you to take any page using Jmol and pop into it a
version of Jmol of your choice. For example:
to the size that I'm exporting to, then I can render
at that size. I tried this, and it works. But what if I need resolutions
that are larger than my screen size (e.g. for printing)?
cheerios and wheaties
-j
Robert Hanson wrote:
This is fixed for Jmol 11.9.10 and Jmol 11.8.12
Thanks, Otis! Sounds great.
On Sat, Nov 28, 2009 at 12:58 AM, Otis Rothenberger o...@chemagic.comwrote:
Bob-
UFF Minimization: What a wonderful addition to Jmol! Among other
things, Jmol can now be used as a basic virtual model kit that allows
users to actually construct small molecules in
In this case, we probably just have a slightly different version of NWChem
being used. Jorg, be sure to indicate that when you send me that file. Let's
get this working.
2009/12/1 Angel Herráez angel.herr...@uah.es
This happens at times with pdb files that have the wrong position of atom
IDs
You just use two applets and mouse-synchronize them
On Wed, Dec 2, 2009 at 9:44 AM, Brian Moldover moldov...@gmail.com wrote:
Hello all,
Is there a way to display multiple models contained in a single PDB file as
a set of tiled windows, or something similar, as opposed to the overlaid
It was due to the NWChem output using all lower case for the atom names.
Fixed for Jmol 11.9.10 and 11.8.12.
Bob
On Tue, Dec 1, 2009 at 1:22 PM, Robert Hanson hans...@stolaf.edu wrote:
In this case, we probably just have a slightly different version of NWChem
being used. Jorg, be sure
times? I’m reading the documentation
but obviously not clear on how to do this or I wouldn’t have asked J
*From:* Robert Hanson [mailto:hans...@stolaf.edu]
*Sent:* Wednesday, December 02, 2009 12:13 PM
*To:* jmol-users@lists.sourceforge.net
*Subject:* Re: [Jmol-users] displaying multiple
version of Jmol? application or applet?
On Thu, Dec 3, 2009 at 2:43 PM, Pakhomova, Olga opakh...@odu.edu wrote:
Images saved in .jpg or .pdf format have 0kb (no image). The only way to
get readable image is .png format
I have 64-bit Windows Vista Home OS
*Olga **P*
in the math itself you just use variables names. $xx would be an identifier
for a drawn object or isosurface and would not be appropriate in that
context.
for (var j=1; j20; j=j+1)
var scale=5*j;
zoom scale;
write image 800 600 @{movie + (+j)[-3][0] + .jpg};
end for
On Thu, Dec 3,
I'll see if I can make that clearer. You just use
x = [ [1,2,3],[4,5,6],[7,8,9]]
for the matrix. (You can also define 4x4 matrixes.)
Or if you want to get it from an axis and angle of rotation, say 34 degrees
around the x axis:
x = axisangle({1 0 0}, 34)%-9
Then you just use the standard
And
write t.jpg
does not work?
On Thu, Dec 3, 2009 at 3:11 PM, Pakhomova, Olga opakh...@odu.edu wrote:
Today I have just downloaded 11.8.11 as an application.
Thank you,
Olga
Olga Pakhomova
757-683-8006 office
opakh...@odu.edu
*From:* Robert Hanson [mailto:hans
matrix to it ?
Thanks,
Jeffrey
On Thu, Dec 3, 2009 at 10:47 PM, Robert Hanson hans...@stolaf.edu
wrote:
I'll see if I can make that clearer. You just use
x = [ [1,2,3],[4,5,6],[7,8,9]]
for the matrix. (You can also define 4x4 matrixes.)
Or if you want to get
Jeff, the problem is that you are using Jmol 11.8. No matrices there.
On Fri, Dec 4, 2009 at 2:58 AM, Jeffrey Tseng ytse...@gmail.com wrote:
Hi, Bob
Given that
x = [ [1,2,3],[4,5,6],[7,8,9]]
print x * {1 3 3}
In Jmol
$ print x * {1 3 3}
13.076697
= I believe this number is not
not find the right example for jmolscript. Was struggling
with trying to use jmolscript(script “filename”, “all”) which obviously is
incorrect!
*From:* Robert Hanson [mailto:hans...@stolaf.edu]
*Sent:* Friday, December 04, 2009 11:21 AM
*To:* jmol-users@lists.sourceforge.net
*Subject:* Re
obviously is
incorrect!
*From:* Robert Hanson [mailto:hans...@stolaf.edu]
*Sent:* Friday, December 04, 2009 11:21 AM
*To:* jmol-users@lists.sourceforge.net
*Subject:* Re: [Jmol-users] running a rasmol script
within Jmol:
script APPLET * background red
applies the script to all applets
for (var j=1; j20; j=j+1)
var scale=5*j;
zoom @scale;
write image 800 600 @{movie + (+j)[-3][0] + .jpg};
end for
On Fri, Dec 4, 2009 at 2:31 PM, Paul Hanson sidewinder70...@mac.com wrote:
Hi,
Thanks for the response to my previous post (see below)! I THOUGHT that
might be the
William,
Yes, that's right. Nested arrays are not supported in Jmol. The only nested
arrays you can do are specifically 3x3 and 4x4 matrices, which have their
own special data types. But arrays of points are supported, so the simple
fix here is to use
$ x = [{111,222,0},{333,444,0}]
$ print x[1]
We don't import electrostatic surfaces from Spartan. The charges are there,
though, so you can at least create your own mapped isosurfaces.
isosurface sasurface 0 map property partialcharge
On Sat, Dec 5, 2009 at 9:43 AM, André Triebel atrie...@hotmail.de wrote:
Hi,
I've been trying to
This is fixed for Jmol 11.9.11 and Jmol 11.8.13. Thank you very much for
pointing this out to us.
On Wed, Dec 9, 2009 at 12:38 AM, suzu hiro111s...@gmail.com wrote:
Dear Jmol developers,
Biomolecule filter doesn't work on recent versions.
command:
load
Maybe you are just loading files (older ones?) that do not have site
information. It works with
$load =1blu
$ show variables
@site_1 ({127:132 157:164 265:270 287:292 342:347 357:362});
@site_ac1 ({53:66 75:88 96:101 208:219 386:398 414:427});
@site_ac2 ({127:132 157:164 265:270 287:292
you can get a mouse down with clickCallback. See
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=2
On Fri, Dec 11, 2009 at 3:17 PM, Otis Rothenberger o...@chemagic.comwrote:
Hello-
On a page with several Jmol applets, I'm trying to use a mousemove
into the applet to detect the
I can't reproduce this on my machine -- they behave properly for me. Anyone
else confirm this? Eric, can you send me a script that fails or set that up
on a web site for us?
On Sat, Dec 5, 2009 at 4:33 PM, Eric Martz ema...@microbio.umass.eduwrote:
In Jmol 11.8.9 and 11.9.10, I see a bug where
On Mon, Dec 14, 2009 at 12:55 PM, Thomas Stout thomasjst...@gmail.comwrote:
I believe that I have just stumbled into either an oversight, a bug or --
most likely -- my not keeping up with version changes...
Anyway, I recently decided that it was time to consider upgrading a
(private) site
-- other than my missing the fact that it removed translucent
objects.
Thanks Bob!
-Tom
On Mon, Dec 14, 2009 at 2:05 PM, Robert Hanson hans...@stolaf.edu wrote:
On Mon, Dec 14, 2009 at 12:55 PM, Thomas Stout thomasjst...@gmail.comwrote:
I believe that I have just stumbled into either
Thanks, Eric. That's fixed for Jmol 11.9.11 and 11.8.14
On Mon, Dec 7, 2009 at 6:43 PM, Eric Martz ema...@microbio.umass.eduwrote:
I am trying to call a state script from within another script.
The state script includes the command initialize which makes
_height and _width undefined. Is this
OH, funny! OK
On Tue, Dec 15, 2009 at 3:55 PM, Thomas Stout thomasjst...@gmail.comwrote:
Hi again --
The combination of zshade translucent surfaces is working great in
11.9.11 -- thanks Bob!
I've just stumbled into one more oddity: after putting the display into
side-by-side stereo,
That's fixed for Jmol 11.9.12. See
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
On Tue, Dec 15, 2009 at 4:01 PM, Robert Hanson hans...@stolaf.edu wrote:
OH, funny! OK
On Tue, Dec 15, 2009 at 3:55 PM, Thomas Stout thomasjst...@gmail.comwrote:
Hi again
Not a bug -- you can't use var on the command line -- it's local to the
script it is given in, and the command line is a single script unto itself.
Only use var within a larger script.
On Tue, Dec 15, 2009 at 4:03 PM, Eric Martz ema...@microbio.umass.eduwrote:
I find that the statement var
cool! First thing to do is upgrade to Jmol 11.9.12. This will allow you much
flexibility in terms of contour lines. 11.8 is not going to get you anywhere
further than this.
Bob
On Tue, Dec 15, 2009 at 5:07 PM, Jonathan Gutow gu...@uwosh.edu wrote:
Dear Jmol Users,
I'm trying to help
15, 2009 at 5:13 PM, Robert Hanson hans...@stolaf.edu wrote:
cool! First thing to do is upgrade to Jmol 11.9.12. This will allow you
much flexibility in terms of contour lines. 11.8 is not going to get you
anywhere further than this.
Bob
On Tue, Dec 15, 2009 at 5:07 PM, Jonathan Gutow gu
Jason,
Oh, good. I'm eager to see you implement controur lines this way, because I
think it will be a general solution to the problem of contour lines we
discussed earlier, and it will look as good or better than gnuPlot ever did.
Basically you don't have to calculate the contour line segments
wrote:
Date: Tue, 15 Dec 2009 17:51:06 -0600
From: Robert Hanson hans...@stolaf.edu
Subject: Re: [Jmol-users] first peak at update to Jmol in SAGE (3-D
functionplotting)...
To: jmol-users@lists.sourceforge.net
Message-ID:
ba9c0bd60912151551p22f1c7c1lae292641b42cb
Jonathan and Jason,
This is a great starting point for a list.
1) An arbitrary number of isosurfaces, with attributes color,
transparency, visibility, mesh color, mesh visibility, lighting state
(fullylit default). The range for the numbers in these isosurfaces
should be limited only by
Rich,
Good point.
Yes, yes. I was just thinking the same thought this morning myself. It's
nice that the Sage community has caught on to how useful Jmol is for general
surface display. If the Jmol community, though, feels that displaying data
in graphical form is outside the bounds of the
and/or be interested in. I think having flexible 3D surface
descriptors and routines may prove to be very useful in ways that may not be
fully appreciated as yet -- I'd vote for keeping it all in one package for
the time being!
-Tom
On Wed, Dec 16, 2009 at 12:22 PM, Robert Hanson hans
.
Bob
On Thu, Dec 17, 2009 at 2:44 AM, Egon Willighagen
egon.willigha...@gmail.com wrote:
On Wed, Dec 16, 2009 at 9:22 PM, Robert Hanson hans...@stolaf.edu wrote:
But I agree, the business with axes and tics and such is pretty far
afield
of the core Jmol mission.
Not sure if ticks
Interesting. inline data is not a recognized data header. I'm surprised
Jmol is saving that in the state. What version of Jmol is this? (Could be a
difference with 11.8 vs. 11.6, I suppose.)
generally to get the data you would use
var data = jmolScriptWait(show data)
Bob
On Thu, Dec 17, 2009
On Fri, Dec 18, 2009 at 9:04 AM, Ralf Stephan r...@ark.in-berlin.de wrote:
...it can read its own format, described here officially:
http://jedi.ks.uiuc.edu/~johns/raytracer/papers/tachyon.pdfhttp://jedi.ks.uiuc.edu/%7Ejohns/raytracer/papers/tachyon.pdf
Well, it's pretty crude. The surface
0 0}
measure ticks {1.0 0.2 0} format [%0.0f] first -1.3 {-3 0 0} {3 0 0}
boundbox off;measures delete;
axes ticks x {2 0 0} format [%0.0f] scale 2
axes ticks y {1 0 0} format [%0.0f] scale 1.5
axes ticks z {3 0 0} format [%0.0f] scale 3
On Thu, Dec 17, 2009 at 12:21 PM, Robert Hanson hans
Is the script coming from a save of the state? I don't see how Jmol is
saving that data in the state, so I must be missing something. It is not
supposed to save data in the state.
Send me the state.
Bob
On Fri, Dec 18, 2009 at 10:21 AM, Jonathan Gutow gu...@uwosh.edu wrote:
Otis,
, 2009 at 10:41 AM, Ralf Stephan r...@ark.in-berlin.dewrote:
On Dec 18, 2009, at 4:27 PM, Robert Hanson wrote:
On Fri, Dec 18, 2009 at 9:04 AM, Ralf Stephan r...@ark.in-berlin.de
wrote:
...it can read its own format, described here officially:
http://jedi.ks.uiuc.edu/~johns/raytracer/papers
obsolete! Thanks). So I think it is appropriate that they
be included in the state.
Jonathan
On Dec 18, 2009, at 12:07 PM, jmol-users-requ...@lists.sourceforge.net
wrote:
Date: Fri, 18 Dec 2009 10:27:09 -0600
From: Robert Hanson hans...@stolaf.edu
Subject: Re: [Jmol-users] Need help passing
to me, but doesn't work when passed. I'm going to
try parsing it to convert to the vertical line syntax for inline data.
Jonathan
On Dec 18, 2009, at 10:25 AM, jmol-users-requ...@lists.sourceforge.net
wrote:
Date: Fri, 18 Dec 2009 09:21:36 -0600
From: Robert Hanson hans...@stolaf.edu
New features for Jmol --
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
35. scales for axes, boundbox, measures * Jmol 11.9.12 adds optional scales
to axes, boundbox, unit cells, and measures. There are three levels of ticks
- major, minor, and subminor. Only the major ticks have labels.
Jmol users:
States, though saved properly in these versions will not be restored to the
proper orientation. This is fixed in Jmol 11.8.14.
Sorry about that...
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
Daniel,
first, it's important to have the two brackets without whitespace:
[[
not
[ [
I know, why should that be, right?
second, for rotateSelected you need to indicate that you want a MOLECULAR
rotation, not one that is defined by the window.
The code is:
r = [[ 0.49441794888,
On Mon, Dec 21, 2009 at 1:43 PM, Daniel Lundin
daniel.lun...@molbio.su.sewrote:
Robert Hanson skrev:
Thanks a lot for your quick reply.
Daniel,
first, it's important to have the two brackets without whitespace:
[[
not
[ [
I know, why should that be, right?
Well
I doubt anything is going to help with JavaScript. Although if you go to the
standard JavaScript syntax:
if (..) {
...
} else {
}
Jmol now supports that. And it's possible that some IDE will at least tell
you where your braces are unmatched.
On Mon, Dec 21, 2009 at 5:54 PM, Thomas
probably need to work on converting to that syntax. I
guess I'm glad (??) I'm not missing something that would make this all much
easier...
-Tom
Sent from a tiny virtual keyboard.
On Dec 21, 2009, at 6:42 PM, Robert Hanson hans...@stolaf.edu wrote:
I doubt anything is going to help
Robert Hanson compares this feature to POV-Ray, i.e. a
specialized feature for the experts. I would disagree with that. Unlike
POV-ray, interactive graphics provides something fundamentally new to the
user and would be used a lot if it is easy to use (from what I can see
JReality
I'm sure you always needed parentheses around that clause on the outside:
if (something) {then do this}
just like JavaScript.
so in this case
$ bigres=40
$ if ({resno bigres}.size 3) {print {resno bigres}.size}
45
On Tue, Dec 22, 2009 at 5:24 PM, Thomas Stout thomasjst...@gmail.comwrote:
That's intentional. All the settings such as zshade, depth, slab, zoom, and
orientation are all reset upon file loading. You can set a defaultLoadScript
to run if you want to do this sort of thing automatically.
Bob
On Wed, Dec 23, 2009 at 12:57 PM, Thomas Stout thomasjst...@gmail.comwrote:
Excellent! I've been interested in working with someone on surface depiction
-- it's one of the areas Jmol is not totally set up for.
Please send us some file examples, and we can see what we can do. And share
with us a bit about the sort of rendering that you would love to have but
maybe don't
This is fixed for Jmol 11.9.13 and Jmol 11.8.15
On Fri, Dec 25, 2009 at 1:27 AM, jaime.prilu...@weizmann.ac.il wrote:
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
Did I forget to send this?
This video demonstrates a first go at incorporating multi-touch capability
into Jmol.
http://www.youtube.com/watch?v=7x8uDRQKIg0
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
special C++ driver I modified that taps a DLL from the screen manufacturer
NextWindow
On Sat, Dec 26, 2009 at 7:53 AM, Egon Willighagen
egon.willigha...@gmail.com wrote:
On Fri, Dec 25, 2009 at 5:01 PM, Robert Hanson hans...@stolaf.edu wrote:
Did I forget to send this?
This video
select atomno = xxx and atomno =
On Wed, Dec 30, 2009 at 2:42 AM, Aya a...@iit.edu wrote:
Hello,
I need to select a range of atoms using their atomno. When I use, for
example, select(*)[first atom no.][last atom no.], it seems to be
shifting the selection by some 14 atoms.
When I
,
Happy New Year, and thanks for any help,
steve
Robert Hanson hans...@stolaf.edu 01-Jan-10 7:32 PM
select atomno = xxx and atomno =
On Wed, Dec 30, 2009 at 2:42 AM, Aya a...@iit.edu wrote:
Hello,
I need to select a range of atoms using their atomno. When I use, for
example
, {0 0 1})
script compiler ERROR: invalid expression token: hkl
select within(3.0,
$
Jmol is version 11.8.15,
Happy New Year, and thanks for any help,
steve
Robert Hanson hans...@stolaf.edu 01-Jan-10 7:32 PM
select atomno = xxx and atomno =
On Wed, Dec 30
Nice! Let's see if we can tighten that code up a bit
On Sat, Jan 2, 2010 at 3:35 PM, Jonathan Gutow gu...@uwosh.edu wrote:
Dear Jmol Users:
(What I did on my holiday break...:)) As part of my work on the Jmol
interface for the SAGEmath project, I have put together a color picker
Dear Fendy -- please send a few sample OUTCAR files so we can see what you
are talking about.
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we
most of the time the administrator
of this mailing list didn't allow my email containing the OUTCAR file
containing the OUTCAR file to pass away to the mailing list.
How do you think robert??
GBU
--
*From:* Robert Hanson hans...@stolaf.edu
*To:* jmol-users
...GBU
--
*From:* Robert Hanson hans...@stolaf.edu
*To:* jmol-users@lists.sourceforge.net
*Sent:* Sun, January 3, 2010 8:06:53 PM
*Subject:* Re: [Jmol-users] How to add bonds for inorganic compoud from
the OUTCAR file of VASP
You-send-it http://www.yousendit.com
--
*From:* Robert Hanson hans...@stolaf.edu
*To:* jmol-users@lists.sourceforge.net
*Sent:* Mon, January 4, 2010 8:45:43 PM
*Subject:* Re: [Jmol-users] How to add bonds for inorganic compoud from
the OUTCAR file of VASP
Actually, these files are small -- all you had to do was zip them up
If you mean, is there a menu-listener option, the answer is yes. What you do
is
set debugScript
and then establish a scriptCallback. Usually scripts run from the menu are
in quiet mode, but this debugScript option disables that and reports them
anyway.
As for setting radius based on BFactors,
Happy New Year to all Jmol users!
Miguel reminds me that it's been almost 5 years since Jmol took over my
life. Can it be that long? My how time flies when you are having fun.
I'm working on crystallography this month. So if you have ideas in that
regard, do speak up. Jmol 11.9.17 has some
Go for it! Some quick ideas:
color picker
MO picker
Xtal symmetry picker
model picker
animation controls
message report box
command line input (already in Jmol.js)
interactive flot graphics for energies -- sort of like
http://chemapps.stolaf.edu/jmol/docs/examples-11/jmol-flot-energy.htm
or other
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