Dear Jmol users,
The pop-up menu has some entries under Select Hetero that I'd like to reword.
- They are only fully understood by those knowing the script language (and the
popup menu
should be clear for naive users)
- In English, some are redundant
- In other languages, they are confusing,
Hi Tom
This all dates back to compatibility with Rasmol and Chime scripts. Rasmol was
designed to
be used mostly with pdb files, and Jmol 10 wanted to inherit that functionality
(which is just
wonderful for us biochemists ;-) ).
So, these are Rasmol tokens that shouldn't change, but I think
You have a point, Rich, but what kind of options could we have for nonprotein
molecules?
There is select by element and by symmetry already. The list of selectable
elements could
be certainly expanded (ideally, to cover all elements present in the model, as
it is done for
amino acids).
The
Hi Henry
At least for echos, it can be done. I let you find about labels:
http://biomodel.uah.es/Jmol/multimodel/11-1.htm
click a button to load a model and you'll see all sorts of funny symbols at the
right inside the
applet
I reckon the way is unicode, not html codes
right -- just use unicode.
And it seems that you need to enclose it in double quotes --at least in my
tests today--
label C\u03B1 # shows just that
label C\u03B1 #shows C and alpha
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Hello, Norwid
We have had little experience with production of PDF files, so your
experience will be very helpful.
The output should display atoms and bonds as they are rendered in
Jmol when you invoke the export. It is certainly possible to have
some atoms as ball stick, others as
If this can be implemented, I think it needs to be done for both the app and
applet. This
could be a way:
* for the app, similarly to what is done for macros (a little known feature of
Jmol app, with its
own menu entry; macros are stored as text files in the user's home folder,
which is
I don't think so, Jonathan. Better to have such thing done
consciously.
Also, if I want to delete a view from the list, I must select it
first. If the view in Jmol changes automatically, then I've lost the
view I had in favour of one I do not want to keep.
I think it is OK as it is now.
Hi Chuck
I cannot reproduce what you see, so I must understanding something wrong.
Can you provide the sequence of scripts that you are using?
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El 9 Feb 2010 a las 9:06, Jonathan Gutow escribió:
Angel,
I'm not sure I understand this objection.
Sorry to have disturbed you ;-)
1) When the user selects a single instance in the webexport list of
instances, the viewer reloads that instance.
That's what I understood.
Jmol 11.9.28 app
After calculate hydrogens, minimize does nothing and locks any
further commands (even zap doesn't do anything)
minimize addhydrogens produces the same lock
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Otis wrote:
If you are after a web application, I don't think there's an
alternative, but do you know Avogadro? It's an app, lets you build 3D
molecules in real time.
The clean up at the end of my current routine is really not bad
visually. I had to do it to keep the growing molecule in
It seems that minimize does not work after set picking deleteatom has been
used
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Hi Albertsson
Using a script:
http://chemapps.stolaf.edu/jmol/docs/#writemodel
says only selected atoms are saved
From the popup menu, I think you can only do this in MOL format:
Show Extract MOL data
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Can you define more precisely what is you are doing to position according to
the boundbox?
Jmol has, since ancient times, commands to orient according to Top, Bottom,
etc, which I'd
say are related to the boundbox. In fact, I've never seen much advantage in
having them in
the menus for
Hi Andrew
Yes, that's an uncoommon format which reader might have some problem.
But first, have you tried with the Jmol app included in the
distribution? We should know first if it's a problem with your
compilation.
The syntax is not correct:
measure RANGE 1.8 3.2 (within(molecule,_F)) (not within(molecule,_F))
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Rob, Nico is the man for your problem.
From what I've experienced and guessed, yes, the standard build script does
not make the
signed applet. It may have to do with what/how/who holds the signature.
I think there's some advice somewhere as to how to apply your own signature
when
building.
I am trying to generate a molecular isosurface for a set of atoms in the model.
Before, by default any isosurface made with isosurface select(myAtomSet) was
open.
Now I find that the surface is closed around the atom set, despite I have bot
set an ignore
option.
Is this a change, or a bug? I
Ah. numeric chain IDs! They are not common, so this passes
unnoticed.
Charles, that's probably a bug, but I guess you can safely remove the
dot asterisk part and get the same result you are expecting
select {[GLY]100:V or [THR]1:2}
# 2 atoms selected
scriptcompiler ERROR: unrecognized
Bob, it's on the email subject:
2b9n.pdb
one of the ribosome ones
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An idea just popped up for Eric:
As a roundabout solution:
Maybe you could load just the selected frames, in the desired order, using
load models
and then animate them?
So,
http://proteopedia.org/wiki/index.php/Sandbox_5_Eric_Martz I would like to
animate just 2 frames, 1.1 and 1.10.
load
Hi Alan
Maybe you can use this:
http://www.stolaf.edu/academics/chemapps/jmol/docs/#setbondstyles
set bondTolerance (decimal)
When autobonding, the value of bondTolerance is added to the two bond radii
of atoms
being tested for a bond. A larger bondTolerance allows atoms that are further
Hi Nick
I think you can do it by including the model/frame spec in the atom expression,
either */1,
*/2 syntax or model=1.1, model=1.2
Say
connect 1.0 1.2 (carbon and model3) (hydrogen and model3) single
connect 1.0 1.2 (carbon and model=3) (hydrogen and model=3) partial
connect 1.0 1.2
I'm guessing, but I see 2 potential problems there:
On 3 Mar 2010 at 20:42, Rolf Huehne wrote:
Let's assume an initial size of 600x600 pixel. Then the browser zoom
setting is changed to 130%. Now the applet is 780x780 pixel. But CSS
will still report 600x600 pixel.
Have you checked that?
El 5 Mar 2010 a las 8:58, Robert Hanson escribió:
Jeff, be sure to check that out with 11.9 and get back to us.
If it's of use, I tried with 11.9.29 earlier today and it fails as
Jeff describes.
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Hi Durga
Search the online scripting documentation for colorscheme. That's
what you need. Apart from the standard schemes, I'm quite sure you
can impose your own. You may need to use a JmolScript variable for
that, I'm not sure.
Piero, you must be careful with the quotes. Javascript gets confused
Try this way, combining double quotes (for Jmol) and single quotes
(for JS):
function setPackaging(){
jmolScript('load {' + parseInt(document.pack.par_a.value) +
parseInt(document.pack.par_b.value) +
Hi Andy
I'm not sure I understand what you mean by adding a trajectory point (I haven't
worked with
trajectories), but regarding the addition of atoms without generating new
frame/model, there
is
set appendNew false
Don't know if that would fix the slowness.
Robert Hanson wrote:
was there a question here?
The question is in the email subject line, Bob.
Charles, that PDB file only has alpha carbons for the Y chain. Not Jmol's fault.
The model has just 5A resolution, so it seems that the whole protein has not
been solved.
1.select an atom in a pdb file and make it the center of rotation
see Scrpting Documentation, commands select and center
2.restrict rendering to only those atoms or structure at a given
radius away from the selected atom (center of rotation)
select within
and then
display
Maybe change the color, or the traslucency
You also have halos
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I don't recall the exact parameters now. See
file:///C:/jmol-dev/workspace/Jmol-
documentation/script_documentation/index.htm?ver=11.10search=callback
#setcallback
There's also a bit of info that may be helpful about how to deal with
callbacks at
Piero,
always starting from
http://chemapps.stolaf.edu/jmol/docs/
(which is linked from Jmol's website)
so
http://chemapps.stolaf.edu/jmol/docs/index.htm?ver=11.10search=callback#setcallback
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I've never attempted f(w,x,y,z) directly, but you can assign custom properties
to atoms, so the
xyz could be coordinates and the 4th datum be assigned to a property, and later
used e.g. for
a color.
See atom properties in the Scripting Documentation
Hi Peter
Yes, Jmol can open .gro files. I'm not sure though if there is more than one
format output by
GROMACS.
http://wiki.jmol.org/index.php/File_formats/Coordinates#GROMACS
I used gro files coming from a molecular dynamics calculation once, but at the
time Jmol still
couldn't cope with
Hi Frieda
I don't think you can do it for any two applets in one go. Either one or all.
I'm assuming you use Jmol.js.
jmolScript() takes as its 2nd argument the ID, which may be all.
For buttons, you need to use jmolSetTarget() which I'm not sure if it accepts
the special all,
but give it a
Piero,
Sorry, I'm lost. Please be specific about what you have and what you
need to do
El 6 Apr 2010 a las 13:09, P.Canepa escribió:
Rob, Angle
I did as you said. What I see is: the file location as b, the name of the
file as c and the title of the file as d.
What's the way to
Hi Umanga
That would be a hyperlink pointing to the pdb file URL. With a
button, the equivalent is location.href
But whether that is downloaded or opened in the browser, or in a
helper program, will depend on each user's browser and configuration.
Maybe you can copy the link present in the PDB
Hi Otis
Quite an impressive piece of work. Congratulations!
In case you want to look into this, my Firefox 3.6 (WinXP) refuses to
show the video at
http://www.che.ilstu.edu/osrothen/web_molecules/video/VMKquickstart.ht
ml
Says I should upgrade my Flash Player, but it is the latest
10.0.45.2.
On 10 Apr 2010 at 18:53, Hans U Wagner wrote at SourceForge.net :
Initial Comment:
Hi, I didn't find any possibility to display formal charges of a molecule.
One of our problem molecules is ozone O3. In our lectures we must use two
mesomeric resonance formulas such as O(-) - O(+) = O -
As far as I remember, this has always been the behaviour, since
Rasmol times.
Apart from the possibility that this may be implemented as a new
feature, there is the dirty trick of using fake bonds (connect
partial) or the less intrusive one of drawing lines (draw). Both
allow setting the
Dear Jmol users,
There is a new link for Jmol Events in the main page of the Jmol Wiki (Jmol
Community
panel). Please feel free to add there your own news and links.
I've just added some information on the Jmol workshops we are organizing at the
beginning
of August within the 21st Biennial
Today I am seeing Java warnings regarding security when I open any of
my pages with Jmol applets, both local and from web server.
That's Java 1.6.0_20 in WinXP (I may have updated Java recently, but
I don't remember for sure when)
The warning says something along the lines of
Java has detected
Thanks, Nico
No, my pages use the unsigned applet with Jmol.js. This problme
wasn't there before, they are old pages.
The applet version is different in different pages:
10.00.58
11.0.3
11.4.RC6
11.9.29
All give the same message, so it's not Jmol version.
El 19 Apr 2010 a las 17:20, Nicolas Vervelle escribió:
Can you still check the status of each jar of Jmol distribution you
are using with jarsigner ?
I'll try to do that
Where do I get jarsigner?
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I've just had the same warning in two non-Jmol pages.
It's the same warning dialog shown at
http://java.sun.com/javase/6/docs/technotes/guides/jweb/mixed_code.htm
l
Definitely a Java update issue.
java.vendor:Sun Microsystems Inc.
java.version:1.6.0_20-b02
os.name:Windows XP
Same in all my
Mmmm... guess what
My computer at home had 6u15 and gave no errors. I've just updated to 6u20 and
still no
problem.
I will further investigate this issue tomorrow when I'm in the office again.
Sorry for having disturbed you all.
This evening I had the same problem in at least 3 sites with
Hi Bin
http://wiki.jmol.org/index.php?title=Troubleshooting/Java_Problems
I was wondering there is an automatic way to do that? That is, users do not
need to clear java
cache manually.
I don't think so, but doing this is not regularly necessary.
What is the problem (display issue) you
OK, problem solved, but no clues as to the cause.
1. It was not a Jmol problem; I saw it with other applets.
2. It was a problem only in one of my 2 computers. But there are
reports in the web of the same problem. One of them says some of our
users are observing it, others not.
3. I cleared
Hello, Francois
However I can´t find the way to get the data back from jmol as a
molfile.
This was commented a couple of days ago. Only for MOL format, you can
use
getProperty extractModel (atom expression)
(see http://chemapps.stolaf.edu/jmol/docs/)
For any format,
Hello, Javier
I have seen similar things continuously. I have the feeling that all
this is Java's fault. Accented characters in folder names do not get
through properly.
For example, if I open a file by dragging onto the Jmol app window,
and the file path has special characters, Jmol does not
Bob, I've had a look at this. Nice! Now that I have all my pages converted
manually ;-)
I am adding some features to the conversion: plugin/applet size in percent,
default rendering
style, ...
There's also the difficult isuue of zoom.
Could you put the JmolToChime.js in the SVN system so we
I think it's just something to add to the replacement text.
script = script.replace(/boundingbox/g,boundbox)
I really don't want to add any Chime synonyms at this point.
I understand. The problem is, that word appears in an spt file, and I haven't
yet figured out
how to parse that.
Wayne, I do not see the reset;center line you mention.
Can we have a look at your molecular file?
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Dear users,
As Bob said, this is coming a bit too late for us and it is more of a
proof-of-concept. Anyway,
I've done some some additions to Bob's ChimeToJmol.js and now this file is
included in the
SVN system for Jmol.
Depending on the Chime features of the actual page it is applied,
On 26 Apr 2010 at 14:29, Wayne Decatur wrote:
[...]
The pertinent part is:
#OR
#Follows Z-Y-Z convention for Euler angles
reset;center {-9.344042 35.45582 69.35735}; rotate z 171.68; rotate y
94.13; rotate z 137.96;
zoom 117.98; translate y 0.06; set rotationRadius
It's a bug present in the RC9_development version from Bob's site but not in
RC8
downloadable from SF.
The problem should be in
org/jmol/export/___Exporter.java
line 275:
outputComment(moveto command: + viewer.getOrientationText(Token.moveto,
null));
So it must be the
Just for clarification, my testing was done with the app, versions
12.0.RC2, 11.0.RC8 from SF download page. And with the version form
Bob's site, 12.0.RC9_dev
I think there shouldn't be any difference whether it's done from the
applet. The code is common AFAIK
El 26 Apr 2010 a las 20:44, Robert Hanson escribió:
About the reset -- OK, that's from a
show orientation
command. I can't imagine how that is getting into a VRML file. I'm
sure missing something!!
To me, it looks like instead of using
show orientation moveto
(that generates a
That's fixed for the next releases.
Thanks for reporting, Yuri
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Wonderful value, Bob!
Plastic mode, maybe?
I also had trouble last night (WinXP) to see it, the applet didn't
finish loading, but today it is working fine.
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I have mixed feelings about this idea. On the one hand, it is
exciting to think that Jmol could do this. On the other, I'm not sure
if it should expand into this land, or leave it to other software.
Although I have not used it regularly, the most similar idea I know
is Avogadro --open source
I am seeing this as a nice, recent addition in the new.htm
document:
122. select within(BASEPAIR)
# Jmol 12.0.RC5 adds the capability to select atoms based on RNA or
DNA base pairing. Thank you, Neena Grover! load 2qnh.pdb.gz;zoom
300;wireframe -0.4;display rna;select *.P;label %n%r;select
I don't think so. There may have been CG in RasMol, but there was
never any capability that I know of in Jmol to detect hydrogen-bonded
base pairs like that.
Well, certainly no detection of base pairs. That's why I think the
distinction must be made clear. The sets are indeed defined in
Hello, Maurice
Your problem seems to be related to the location of files.
I assume you are testing your page from local disk. Java imposes some
restrictions for
security (this is explained in the docs), so you cannot have your molecule file
in a folder that
is NOT below the folder where the
Hi again, Maurice
Please, use the jmol-users list for replies, so everyone can follow the
discussion (it may be
helpful to others)
On 22 May 2010 at 14:24, Maurice Schroff wrote:
However, I tried to locate the cc.pdb in a sub-directory named
ordner1 and then altered the code:
Hello Jay
Difficult to test ribbons with a one-residue model. I will try to guess:
1. I imagine this is not the case, but you have a call to Jmol.jss (two S
letters)
2. The jmolRadioGroup should take an array of arrays. Maybe it works with what
you have,
but better make all elements
From
http://www.molinspiration.com/jme/doc/jme_functions.html
public void JME.reset()
clears the drawing canvas (deletes all molecules)
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Two cents from this side of the Atlantic:
html
head
script type=text/javascript
function newProblem(){
document.getElementById(JME).reset();
}
/script
/head
body
applet id=JME archive=JME.jar code=JME.class width=400 height=400
param name=jme value=22 23 O 2.80 -9.04 O 4.02 -6.94 O 4.02 -11.14
Maurice, as far as I know Liveweb will just display inside Powerpoint
whatever webpage you have.
From your description, I'm not sure exactly what your problem is, but
I don't think Jmol has anything to do with it.
On the other hand, I find that using Liveweb is not worth the bother.
I'd
You cannot use that syntax
select atomNo=4,8,11,17,14,6
You must use
select atomNo=4,atomNo=8,atomNo=11,atomNo=17,atomNo=14,atomNo=6
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Unbelievable, but true. Where you define the menu, you have
script type=text/javasript
There is a c missing,
script type=text/javasCript
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Hi Maurice
Yes, that how the animation on command works by default. You can change the
delays.
Check the scripting documentation
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Hi Jaime
'set rocketBarrels' is working OK for me in 11.8.23, 11.8.24, 12.0.RC11 and
12.0.RC15
In general, is there an option to remove arrow heads?
(beta sheets, ...)
I don't think so. But I see no reason to be able to remove arrowheads
from alpha rockets and not from beta rockets.
Hi Miguel!
You can draw it and have Jmol optimize 3D
Or draw it elsewhere and optimize 3D (I use ChemSketch) then save and open in
Jmol
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Coolest method:
1. find the SMILES string for 2-propenyl sulfenic acid
2. get the latest Jmol 12.0.RC
3. open the script console
4. type
load $C=CCSO
5. watch the 3D structure appear in Jmol
Kudos to Bob!
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Is there an option for drawing water as crosses instead of spheres?
There is stars. I think you could use it for what you want.
If I remember correctly, Eric uses it in FirstGlance in Jmol.
Is there an option to 'set autobond OFF' only for water?
Don't think so, but maybe you can use
I don't use Pymol, but that doesn't sound bad -as long as it is not
difficult to implement.
By the way, I've recently known about an initiative to set a system
that translates between script languages: Pymol, Rasmol, Jmol are the
first targets. The idea is that you can use the scripting
El 1 Jun 2010 a las 7:37, jaime.prilu...@weizmann.ac.il escribió:
It seems that this only works on alpha helices, no effect on beta sheets.
What Bob meant is that he could expand the existing command so that
it affects beta sheets too.
I have no opinion about whether this should be done or
My opinion:
1. I agree that we must stress the recommendation to use the split applet
files. I'll take a look
at the Wiki page to reinforce this.
2. I don't agree about removing the translations from the monolithic applet. If
someone
decides to use it for some reason (e.g. for local testing
Jay, I'm not sure if this is the cause of your problmm but, as a
general rule, Jmol needs double quotes around file names for the load
command (or no quotes at all, as long as the file name and path does
not contain any conflictive characters)
So, try exchanging your double and single quotes:
Make sure to also fix your quotes and parentheses:
You had:
jmolApplet([100%,100%], load
'http://www.rcsb.org/pdb/files/1I78.pdb1.gz');
The double quote before load should be closed before the parenthesis
is closed:
jmolApplet([100%,100%], load
'http://www.rcsb.org/pdb/files/1I78.pdb1.gz' );
Helo Alexander
There is a classical warning that applets should not be resized too
often, but with recent browsers I've never seen any problem in
continuous resize of JmolApplet.
Unless you are somehow setting the size to zero (temporarily).
Depending on the browser, zero-size applets are
Craig,
I'm speaking on some recollection, haven't tested this, but I think you can do
this way:
frame all;
display */2,*/4,*/6;
There shoul also be an alternative model=n syntax of some sort.
Why do you say that display hde do not apply to models? They should
Yeah, there it is:
frame all; display 1.2,1.4,1.6
or
frame all; display model=2,model=4,model=6
or
frame all; display */2,*/4,*/6
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Otis,
I might as well also ask you to remind me what the code is for the
maximum atomIndex. I know that I should not be using the atomIndex=1000
trick.
{*}.atomindex.all.size
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I still need to narrow down the problem, but I'm seeing something
strange with 12.0.RC16 that wasn't there in (quite) previous
versions.
Does it ring a bell or should I go on narrowing the exact
circumstances?
Applet, message callback is active (to report about the ongoing
minimization)
I
Hi Philip
The error message sounds like a Java security I've seen several times. The
browser may be
caching files, sometimes it's difficult to convince it that you have changed
things.
I suggest:
1. first, make double sure that the location of model files and applet files
satisfies the rule:
Further, even accounting for tricky security policies, I cannot
imagine why the very same command works from the console, and what
has minimize to do with the security. (minimize is also failing from
a button, not from console or popup menu)
Well, I don't think that Jonathan's well-based explanation says why
this didn't happen to Phil with a previous version of Jmol.
I see this security rules are a complex situation.
Also, maybe by chance, but I'm having seeming different problems that
come also to Java security issues. I'm testing
This is the summary and a test case:
1. Problem is there only for local files, not from server. Seems to
be related to Jmol reading text files (either scripts or the UFF.txt
file embedded somehow inside Jmol) from a folder where the applet
jars are but the webpage is not.
Main_folder
|
El 8 Jun 2010 a las 12:02, Philip Bays escribió:
Obviously I have to learn to use Jmol.js:-)
Well, that's really easy. But won't keep you away from the cache
problems :-)
Good luck
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El 8 Jun 2010 a las 20:43, Philip Bays escribió:
I set one of my HTML files to call the signed applet. It calls it
and gives me the signed applet dialog. As I look at it I have three
choices -- run, cancel, or always trust. I understand Run and Always
trust. But I assumed that Cancel meant
Bob wrote:
jmolSetCallback(UseCommandThread,true)
Thanks, Bob, that's great!
It fixes the script file loading, but not the minimize from a button.
I'm compiling more detailed testing, but for now (applies to both
Firefox and IE8 in WinXP):
Description of folder locations, relative to the
Jay, any page with Jmol applets should work the same in any browser. And that's
important.
What are the differences you are seeing? What is doesn't work?
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Jay,
There are many wasy you can do that. Several parts:
1. How to pick the color. Simplest is e.g. to have a select control (a
drop-down menu) with
a few colors. The user selects one, the color value is passed to a javascript
variable that will
later be fed to a Jmol script.
A more
one more tip: a different file format, but same idea:
http://biomodel.uah.es/Jmol/amber/
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Bob, I know nothing about the basis of lipophilicity ither than having seen it
a couple times in
Chime, coloring molecular surfaces.
I'll try to check tomorrow some examples in Chime and maybe in Accelrys
Discovery Studio
Visualizer too (don't remember now if it offers MLP, but might be, in
Paul Pillot wrote:
(I haven't
been able to make a smooth scaling from vdw to ball stick for
example)
Paul, how about this?
for (var i=1;i=10;i++) {
y=100-80*(i-1)/9;
spacefill @y%;
z=0.9-0.75*(i-1)/9;
wireframe @z;
delay 0.2;
}
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