ng the lcaocartoons
>>>
>>> Dean, the main reason I'm jumping in here is the display unitcell
>>> command. Is that a legal Jmol Script command? After loading a CIF file, I
>>> thought that you had to do something like this to get the unit cell:
>>>
>
%;
Dean Johnston
On April 10, 2017 at 9:00:03 AM, Pshemak Maslak (p...@chem.psu.edu) wrote:
Can the "slab" command be used to produce presentations equivalent to the
image linked below?
https://en.wikipedia.org/wiki/Atomic_packing_factor#/media/File:CCC_crystal_cell_(opaque).svg
This is listed on the Wavefunction, Inc. web site (
https://www.wavefun.com/products/databases.html):
Spartan Molecular Database (SMD), a collection of over 150,000 calculated
structures and associated properties of molecules, each obtained from as
many as ten different theoretical models
I know that CrystalExplorer (http://hirshfeldsurface.net/) will generate
Hirshfeld surfaces, but I haven’t used it much. It relies on some kind of
wavefunction calculation (Tonto or Gaussian in the case of
CrystalExplorer), so I imagine that Jmol will similarly require more than
just coordinates.
I’ve just started playing around with the CSD Python API
(https://downloads.ccdc.cam.ac.uk/documentation/API/) - seems like Jmol would
be ideal for displaying results from Python-generated searches.
Dean
On July 31, 2015 at 2:21:55 PM, Robert Hanson (hans...@stolaf.edu) wrote:
Q: Has anyone
Eric,
I am not able to completely reproduce this (Mac OS 10.10.2, Macbook Pro 15”,
Mid-2014), but I did notice that on the one display I could not position the
Jmol app higher than a certain point. If I tried to move the app to the top of
the screen, it would just move it about half-way down.
multiple representations of unit
cells for an expanded lattice. In the later version (including 14.1.8), the
unit cells end up spaced out” instead of contiguous. Picture and links below.
Dean Johnston
Jmol 13.3.3 (http://crystals.otterbein.edu/packing/packing-jmol13-3-3.html)
— click on “simple
= jQuery.noConflict();
On Wed, Feb 5, 2014 at 5:33 PM, Dean Johnston djohnsto...@gmail.com wrote:
Jmol users list,
I’ve noticed a change in behavior of the unitcell/draw unitcell command
somewhere between 13.3.3 and 14.1.6. I’m using it to draw representations of
multiple unit cells
Thanks Bob - the simple solution is just to make the main object opaque (it
was already nearly opaque). Then all the translucencies look just fine. I
don't really know why I made it translucent to begin with.
Dean
On Mon, Aug 8, 2011 at 1:35 PM, Robert Hanson hans...@stolaf.edu wrote:
Jmol
Jmol'ers,
I just noticed an interesting effect in Jmol. I have a model with several
planes having different levels of translucency. But Jmol only seems to use
the translucency of the frontmost plane when looking at something that falls
behind two translucent planes. I suspect this is in the
of delete
not... That gives you more flexibility.
Bob
On Sun, Jul 17, 2011 at 9:29 PM, Dean Johnston djohnsto...@gmail.comwrote:
Simon,
Here's what I've used. It obviously only works for molecular systems and
can be somewhat slow for very large molecules/unit cells. Bob can probably
Simon,
Here's what I've used. It obviously only works for molecular systems and
can be somewhat slow for very large molecules/unit cells. Bob can probably
figure out a more efficient way to do this, but it works for me. In these
examples I've deleted any molecules that I don't want to see -
Just like Bob said, on my Mac (10.6.7, Java 1.6.0_24) it depends on whether
it is the signed applet (or stand alone app). With the signed applet or
application, I find it handy to select text from the Jmol console (or the
script editor) and then click and drag it onto the desktop to create a text
Does anybody know if there is a relatively simple way to find all the
crystallographic symmetry elements within a unit cell using Jmol? For
example, if there is an inversion center at the origin, there may be several
other inversion centers generated by the space group symmetry. I can see
some
probably just as well to take a
random point and keep operating on it, returning its unit cell coordinates
each time. Anyway, since you can get the matrices for the space group
operations, you should be able to get all combinations of them.
Bob
On Thu, Apr 21, 2011 at 10:45 AM, Dean Johnston
Excellent - lots of beautiful examples showing why Jmol is a killer app!
Dean
On Thu, Sep 2, 2010 at 3:21 PM, Robert Hanson hans...@stolaf.edu wrote:
*This just in!
*
*J. Appl. Cryst.* (2010). *43* [
doi:10.1107/S0021889810030256http://dx.doi.org/10.1107/S0021889810030256]
*Jmol* - a
the load
command with all its options (append, filter, {n n n}, unitcell, spacegroup,
etc.) with the data command included in it:
load data append inline
..
end data append inline packed {3 3 3}
Bob
On Sat, Jul 24, 2010 at 9:54 PM, Dean Johnston djohnsto...@gmail.comwrote:
Bob
Bob,
Just testing 12.0.RC28_dev and for my site the DATA command with the
append option (set appendNew true) appears not to work properly (models are
just replaced). Sorry I don't have time to do any more detailed testing. I
didn't have to set the appendNew flag in the past - I think in 11.8
I'm having fun playing with all the wonderful crystallography stuff built
into Jmol, but I'm getting the following when I try the ROTATE with the
SYMOP option. It seems to happen with both the applet and the application -
with a variety of CIF files.
Exception in thread QueueThread0
Yep - problem fixed. Thanks, Bob!
On Tue, Mar 9, 2010 at 9:18 AM, Robert Hanson hans...@stolaf.edu wrote:
I think I have this fixed.
On Mon, Mar 8, 2010 at 8:35 AM, Dean Johnston djohnsto...@gmail.comwrote:
I'll post one as soon as I can - my current observations are on a complex
page
, Dean Johnston djohnsto...@gmail.comwrote:
Possible bug with newer version of Jmol (11.9.32).
I'm finding that the arcs that I'm drawing (with the FIXED option) are
popping on and off during animations. This glitch does not appear in Jmol
11.6. Unless the syntax has changed, I think
Possible bug with newer version of Jmol (11.9.32).
I'm finding that the arcs that I'm drawing (with the FIXED option) are
popping on and off during animations. This glitch does not appear in Jmol
11.6. Unless the syntax has changed, I think this might be a bug. All
other objects created using
about 20 lines of code. Fun!
So the solution is to create a sphere isosurface for each.
Kind of neat that the unitcell doesn't have to be orthogonal.
Also works with boundbox.
Bob
On Fri, Feb 26, 2010 at 10:48 PM, Dean Johnston djohnsto...@gmail.comwrote:
Jmol Users,
Here's something
, we can talk about another way of doing it, but for
now this should work.
Bob
On Wed, Mar 3, 2010 at 7:44 AM, Dean Johnston djohnsto...@gmail.comwrote:
Oh - this is great! Exactly what I wanted - in a straightforward
implementation - nicely done. Thanks Bob!
Dean
On Tue, Mar 2
Jmol Users,
Here's something I've always wanted to do with Jmol -- use clipping planes
to show students the *fractions* of atoms in a unit cell (similar to
attached image of NaCl generated using POV-Ray). I know I can use slab HKL
and depth HKL, but those don't slice through the atoms like the
I haven't noticed any severe problems with the testing I've done (WinXP SP3,
IE7 and IE8). But I spend most of my time with Firefox.
Dean
On Sun, Oct 4, 2009 at 7:54 PM, Robert Hanson hans...@stolaf.edu wrote:
In case it's any consolation -- Windows 7 running MSIE 8.0.7100.0 works
just fine.
background color. If you can avoid the white/black switch, perhaps it won't
be so noticeable.
On Wed, Apr 1, 2009 at 9:44 PM, Dean Johnston djohnsto...@gmail.comwrote:
Jmol users,
Has anybody else noticed the Jmol applet blinking (flashing black) when
being scripted via Javascript in Safari
I don't know if this will work for your situation, but I use a Firefox
extension called Web Developer (
https://addons.mozilla.org/en-US/firefox/addon/60). It adds a toolbar that
allows you to temporarily disable the cache (along with many other useful
features).
Dean
2009/4/2 Angel Herraez
Jmol users,
Has anybody else noticed the Jmol applet blinking (flashing black) when
being scripted via Javascript in Safari? I've had some users complain with
my website (http://symmetry.otterbein.edu/gallery), but I'm not sure if it's
something specific I'm doing. It can be rather distracting
I've used the Prototype.js library pretty extensively in my pages (
http://symmetry.otterbein.edu). I store my structures as JSON files which I
can read and evaluate using the AJAX functionality in the prototype
library. I also do some select DOM replacement to generate tables of
checkboxes and
different applet windows. Sort of a
dummy applet idea. You would do all control on one, but the matching
stereo image would be sent to the other.
Bob
On Mon, Nov 24, 2008 at 8:01 AM, Dean Johnston [EMAIL PROTECTED]
wrote:
Thanks for the clarification. I think I'll go for the slight
), and then turn mouse syncing back on.
They will now track properly as stereo images.
On Sat, Nov 22, 2008 at 9:22 PM, Dean Johnston [EMAIL PROTECTED]
wrote:
Bob,
I guess I was asking if the sync command could be modified (feature
request!) such that two different perspectives could
how he does it. I'm
pretty sure you just make the applet or application 2048 pixels wide
and then direct the left side of the screen to one projector and the
right side to the other.
Bob
On Fri, Nov 21, 2008 at 9:15 PM, Dean Johnston [EMAIL PROTECTED]
wrote:
Jmol users,
I've had
Jmol users,
I've had a request to make my Jmol pages work with a GeoWall-type setup.
(If you're not familiar with GeoWall (www.geowall.org), it's a low-cost
stereo projection system. You setup a computer with a dual-head video card,
two projectors with polarizing filters, and align the two
Just confirming that the fix works for me. Thanks Bob.
Dean
On Sun, Oct 5, 2008 at 8:20 PM, Robert Hanson [EMAIL PROTECTED] wrote:
this is fixed for Jmol 11.6
On Sat, Oct 4, 2008 at 12:20 AM, Dean Johnston [EMAIL PROTECTED]wrote:
Here's an odd one. My (very short) translucent cylinders
, Robert Hanson [EMAIL PROTECTED]wrote:
ok, that should be a simple fix. simple Jmol script?
On Fri, Sep 26, 2008 at 1:17 AM, Dean Johnston [EMAIL PROTECTED]wrote:
Bob,
I'm finding that my state script doesn't properly reproduce the scale
of the arcs. They should be the same size
I can view it (using QuickTime player) on a Mac (OS X 10.5.5). It shows up
as a 500x500 movie - looks pretty good to me and plays very fast (it's done
within less than 5 seconds).
Dean
On Wed, Oct 1, 2008 at 10:25 AM, Robert Hanson [EMAIL PROTECTED] wrote:
Question: Can you watch this movie
http://www.chemtube3d.com
Tel: +44 (0)151-794-3506 (3500 secretary)
On 3 Oct 2008, at 00:06, [EMAIL PROTECTED] wrote:
Message: 3
Date: Thu, 2 Oct 2008 16:03:58 -0700
From: Dean Johnston [EMAIL PROTECTED]
Subject: Re: [Jmol-users] Creation / representation of aromatic bonds
Here's an odd one. My (very short) translucent cylinders disappear when
viewed within a few degrees of edge-on. To be more exact, the center
disappears while the edge remains visible. These are the same type of
cylinders that are generated by the draw pointgroup command. I've only
started to
I don't know if this is a bug or a feature, but my script to display a model
of benzene ends up with all double bonds. Here is a snippet of the script
(the structure is defined via an inline data file):
set autobond false;
data model benzene | ... (atom coordinates here) ... |end model benzene;
Have you tried 'calculate aromatic'?
Regards,
Rolf
This message was sent using IMP, the Internet Messaging Program.
Yes, but in my case that produces alternating double bonds and dashed single
bonds - not a representation
Bob,
I'm finding that my state script doesn't properly reproduce the scale of
the arcs. They should be the same size as the disks (see the attached the
Jmol state file). If this has been fixed since RC_12 then ignore this.
Dean
# Jmol state version 11.6.RC12_dev 2008-08-14 16:55;
#
Dear All,
Has anybody noticed a change in the console behavior for the applet between
RC12 and RC17? I don't know if this is specific to OS X. I used to be able
to select text from the applet console and drag it either to the desktop (to
create a text clipping) or to the console of the Jmol
Dear All,
I've been playing around with some of the molecular math features of
Jmol - it's truly amazing how easy it is to analyze a large number of
structures. My only difficulty has been getting the results out to a simple
text file.
At first I tried copying the text from the console -
I can't reproduce this - the javascript command works just fine from the
Jmol console for me on both Firefox and Safari for OS X.
Dean
On Fri, Sep 5, 2008 at 6:18 PM, Eric Martz [EMAIL PROTECTED]wrote:
It appears to me that the javascript command of Jmol does not work in
Safari on Mac OS X.
, that fix is checked in -- problem for any case where there is no
principal axis.
On Fri, Aug 22, 2008 at 9:52 PM, Dean Johnston [EMAIL PROTECTED]wrote:
OK, it's working much better, but a few obscure errors with my test set
(this is with both 11.6.RC10-applet, and 11.6.RC11_dev-application
:
I'm not observing this, Dean. You will have to be more specific -- send a
state script.
Bob
On Sun, Aug 24, 2008 at 9:10 PM, Dean Johnston [EMAIL PROTECTED]wrote:
Dear All -
I've just noticed an odd behavior with the echo command. I've been using
sub (subscript) tags in some of my echos
Jeff,
No apologies needed. Giving an id to a div does not create a Javascript
object automatically (at least in Firefox). You will have to use something
like:
var myText = document.getElementById('jmolText');
and then say
myText.value = dump(_dataInfo);
It's interesting that it *does*
2008 at 10:57, Dean Johnston wrote:
OK, here is the state for ammonia, with a label of Point Group =
Csub3v/sub at the
bottom left. Without the tags the spacing is normal.
Just typing it in the console of 11.6.RC10 app it looks Ok to me
Maybe some combination with other scripts are doing
If you're using Firefox at all, I've found the Firebug plug-in (
http://getfirebug.com/) to be immensely useful. Whether your debugging
Javascript or just want to look at the DOM, it works great for me. Just set
a breakpoint right after your jmolGetPropertyAsArray() call and then find
your array
Dear All -
I've just noticed an odd behavior with the echo command. I've been using
sub (subscript) tags in some of my echos (I think this is an undocumented
feature). At some recent point (after 11.4), any echo'ed text with a sub
tag shows up with extra spaces between the letters. All other
Dear All (but mostly Bob) -
(Sorry about the duplicate message regarding echo - I thought my mail
program never sent it out...)
I'm having problems drawing individual symmetry elements (Jmol 11.6.RC11)
using the format draw pointgroup c2 1
It correctly draws the first element, but then won't
Jeff,
You can certainly avoid using innerHTML. I only ended up using it because
it was the only way to get my particular pages working with Internet
Explorer (arghh). And now that I depend on it I don't bother to avoid it...
In your almost working version, you were sending a Javascript
On Fri, Aug 22, 2008 at 10:01 AM, Robert Hanson [EMAIL PROTECTED] wrote:
found it -- Nico, let's get RC10 out so Dean can test it.
Bob
On Thu, Aug 21, 2008 at 11:21 PM, Dean Johnston [EMAIL PROTECTED]wrote:
This (the write pointgroup draw command) still isn't working for me (RC9
I've just noticed an odd behavior with the echo command. I've been using
sub (subscript) tags in some of my echos (I think this is an undocumented
feature). At some recent point (after 11.4), any echo'ed text with a sub
tag shows up with extra spaces between the letters. All other echos are
)
etc.
On Tue, Aug 19, 2008 at 11:17 PM, Dean Johnston [EMAIL PROTECTED]wrote:
Bob,
write pointgroup draw gives the following error (for 11.6.RC8):
Exception in thread QueueThread0 java.lang.NullPointerException
at org.jmol.symmetry.PointGroup.getInfo(Unknown Source
I'm not sure of the context, but this should be OK if it's part of an *
external* javascript file. If it's within an HTML page, the browser is
interpreting the /script in your string as the closing tag of your script,
thereby rendering everything that follows as HTML.
Dean
On Thu, Aug 21, 2008
Bob,
write pointgroup draw gives the following error (for 11.6.RC8):
Exception in thread QueueThread0 java.lang.NullPointerException
at org.jmol.symmetry.PointGroup.getInfo(Unknown Source)
at org.jmol.symmetry.Symmetry.getPointGroupInfo(Unknown Source)
at
On Fri, Aug 8, 2008 at 8:46 AM, Bob Hanson [EMAIL PROTECTED] wrote:
version=11.6.RC3
# bug fix: minor error in pointgroup
# new feature: draw pointGroup [type] [index] SCALE [x]
# where [type] is one of Cs, Ci, Cn, or Sn, where n is an integer or
the character n
[Dean Johnston, please
Very nice - I like that you can select what to draw and the different
color for the horizontal plane. How is the default scale determined?
(It seems with some molecules [C2h], the planes extend well beyond the
outermost atoms, while with others [Ih], they end in the middle of
some
I will also be presenting at BCCE 2008. While my materials
(http://symmetry.otterbein.edu) don't use all the latest and greatest that
Jmol has to offer, I will certainly sing its praises. I'm looking forward
to some exciting sessions.
Dean Johnston
On 7/23/08 12:40 AM, Bob Hanson [EMAIL
Jmol users,
If anyone is interested, I just tried Jmol on Safari 3.1 for Windows
and it appears to work quite well. (Previous versions of Safari for
Windows just hung up with many Java applets.)
That said, I did find that some pages (in Bob's documentation examples
and Angel's pages) that I
from the menu gives the following in the history:
vector 3
vector scale 1.0
vibration scale 0.5
vibration 0.5
load /home/djohnston/Structures and Plots/ferrocene.mol
console
iron#??
$
Should I submit a bug report on this?
Dean Johnston
I can't reproduce this problem on my system (also OS X 10.4.11). Jmol loads
just fine and all the example scripts appear to work.
Dean Johnston
On 11/28/07 3:44 AM, David Leader [EMAIL PROTECTED] wrote:
Bob wrote:
I've updated
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
Cool! Very nicely done.
Dean
On 10/18/07 1:04 PM, Bob Hanson [EMAIL PROTECTED] wrote:
Robley Light wrote:
Several weeks ago I asked the list if anyone knew of files that could
display geometric shapes (for a lower grade math and science project).
I'd like to thank Bob Hanson and Dean
. For the dodecahedron my site
uses a combination of three-sided and four-sided figures to stitch
together a five-sided face.
I hope this is of some help.
Dean Johnston
On 9/6/07 5:55 PM, Robley Light [EMAIL PROTECTED] wrote:
Its been a while since I've monitored this list, so forgive me if this is a
question
OK, not simple, but very impressive what you can do with the molecular
math. (I especially like the use of improper angles.)
Now, if I want to orient along an line (as opposed to along a bond), can I
do it the same way? Is there a way to extract the endpoints of a line?
When I tried something
. Is what you are asking to do to align some axis in the
molecular system with some axis in the reference plane? In other words,
something like orient the axis going through atoms 1 and 2 along the X
(horizontal) axis?
Bob Hanson
Dean Johnston wrote:
Jmol users,
Does anybody know
lines, since we are painting more triangles than actually needed. Just
the way it goes, I guess
Bob
Dean Johnston wrote:
Has anybody tried to create polyhedra with 12 or 20 vertices? The
documentation seems to indicate that I should be able to go up to 20.
I¹m creating
I could get some relatively simple Java applets to run on Safari/WinXP, but
not Jmol. All the reports I've read say Safari on Windows is pretty
unstable, but I don't know what Java support it's supposed to have.
Dean
On 6/13/07 2:51 PM, Alan Hewat [EMAIL PROTECTED] wrote:
Jobs also confirmed
commands, so I forgot that triangles were that
easy. Thanks!
Dean
Dean Johnston wrote:
OK, I see that the POLYHEDRA command is really overkill for what I'm trying
to do. I could essentially create my own polyhedral representations if the
DRAW command was extended to allow the drawing
manually
from a connection list) after the molecule loads.
For some reason I never get the same error under Windows (Firefox or IE).
If it¹s any help, my earlier version of the page that uses the 11.1.22
applet does not produce the same error.
Dean Johnston
if you want me to put up an example page (it's currently just running
locally).
Dean
On 6/8/07 10:39 PM, Bob Hanson [EMAIL PROTECTED] wrote:
Dean, please send me the script. I'd like to fix this.
Dean Johnston wrote:
I¹m getting an odd (and hard to reproduce) crash with the Jmol applet
Has anybody tried to create polyhedra with 12 or 20 vertices? The
documentation seems to indicate that I should be able to go up to 20.
I¹m creating representations of shapes (Platonic solids, actually maybe
Jmol isn¹t just for molecules anymore... :-). I would like to display an
icosahedron
the script. I'd like to fix this.
Dean Johnston wrote:
I¹m getting an odd (and hard to reproduce) crash with the Jmol applet
(Firefox or Safari on OS X, version 11.1.48_dev). I try and load an
inline model and sporadically get the error listed below. It seems to
always
I had similar problems - On OS X the Java cache is located in
~/Library/Caches/Java/cache you can clear it using the Java Preferences
utility. I always wondered why clearing the browser cache didn¹t always
work when I updated Jmol versions.
Unrelated note has anybody tried inline files using
On 3/18/07, Dean Johnston [EMAIL PROTECTED] wrote:
I can't seem to get set backgroundModel n to work when loading files
using the inline append command with Jmol 11.1.22. It works just fine with
the normal (non appended) inline files. Has anyone else tried this with
appended file sets
Similarly,
data append .end append ;
will insert an inline model into either a new frame or the current
frame, as per the setting of appendNew.
Is it possible to insert more than one new model using data append ?
When I try I get the following:
Exception in thread
are
opaque -- but you can't see the oxygen through the translucent plane.
Dean Johnston
-
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I got it now - works great. The ability to fade in is an especially nice
effect.
Dean
On 3/13/07 10:05 PM, Dean Johnston [EMAIL PROTECTED] wrote:
Bob,
Are you saying we should ask for too much more often? ;-)
I LOVE the translucency - I've been playing around with it using
On 3/7/07 4:17 AM, Angel Herraez [EMAIL PROTECTED] wrote:
A flat ellipsoid?
I wouldn't call that easy, but...
That doesn't really work because isn't a flat ellipsoid (large
eccentricity) just a circle? And you can't really get it totally flat.
You can also create a polygon with as many
Jmol users,
I¹d like to create a representation of a plane that is an ellipse rather
than a rectangle. Is there a simple way to create a representation of an
ellipse in Jmol? Thanks for any pointers / suggestions.
Dean Johnston
it looks like
Mol2Reader.readCrystalInfo must be reading 14 1 instead of just 14.
Should be a simple fix. Bob?
Dean Johnston
-
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I have just checked in a version of Jmol that allows:
inverting selected atoms about points and planes
I like it! I thought about asking to add something like this a while
back, but never got around to submitting an official feature request. I can
think of some really nice ways of using this
WOW! This is what I needed two months ago. You just made about half of my
Javascript code unnecessary, but it's so much easier and cleaner to do it
within Jmol.
OK, I've got rotation, translation, and inversion of selected atoms
going now. It can all be scripted using
rotateSelected
rotating or zooming molecules.
Dean Johnston
Department of Chemistry and Biochemistry
Otterbein College
On 2/13/07 2:19 PM, Jeff Hansen [EMAIL PROTECTED] wrote:
My university is currently trying Moodle as an alternative to Blackboard for a
Course Management System. One of the things I like
load for me.
Dean Johnston
-
Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job easier.
Download IBM WebSphere Application Server
When I try to get to the Jmol Wiki, I get a page that is definitely NOT the
Wiki. Is this just a problem with SourceForge? www.jmol.org gives an error
as well.
Dean Johnston
-
Using Tomcat but need to do more? Need
This is what I see:
The first link (wiki.jmol.org) loads a page that is basically an
advertisement for GoDaddy. Not the Jmol wiki.
The second link (www.jmol.org/wiki) gives a 404 error.
Dean
On 2/13/07 4:53 PM, Nicolas Vervelle [EMAIL PROTECTED] wrote:
Dean Johnston wrote:
When I try
Yes, of course it makes sense now. I'm typically using NOT in the context
of database searching where it is much less mathematically precise. Thanks
for the clarification.
Dean
On 2/13/07 6:18 PM, Bob Hanson [EMAIL PROTECTED] wrote:
Dean Johnston wrote:
I have a file with about 15
The DATA command has stopped working for me somewhere between 11.1.8 and
11.1.12. Issuing the simple command:
data model example|2|testing|C 1 1 1|O 2 2 2|end model example;show data
hangs the applet (says script pending) and starts chewing up processor
cycles.
Observed on OS X and WinXP.
I just switched to 11.1.9 and Jmol no longer colors my objects (planes,
isosufaces, polyhedra) translucent. I can still color atoms and bonds
translucent.
Dean Johnston
-
Using Tomcat but need to do more? Need to support
this might be useful?
Dean Johnston
-
Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job easier.
Download IBM WebSphere Application
Angel,
Thanks - the resolution parameter was the first thing I tried. It was
late and I guess I was entering the parameters in the wrong order.
Dean
On 1/26/07 5:55 AM, Angel Herraez [EMAIL PROTECTED] wrote:
Hi Dean
There is a resolution value for isosurfaces, so I guess your problem
to draw small isosurface spheres, but I want
to draw psuedo-atoms that are about the same size as the atoms in a
ball-and-stick representation.
Dean Johnston
-
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the
illusion of translucency. I have a simple (very artificial) example page at
http://www.otterbein.edu/home/fac/dnhjhns/jmoltest/trans_test.html. In that
example, the oxygen and the plane are translucent and the hydrogens are
opaque -- but you can't see the oxygen through the translucent plane.
Dean
method should work as well... Am I missing
something?
Dean Johnston
-
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