Looking around I see that "JVX" stands for Java View geometry file. JVXL is
probably better?
René, OK, I understand what the code is doing now. I calculate that inclusion of
interpolation smoothing still allows for the inside/outside idea, but along with
that, an accounting is necessary of the fractional distance along each edge of
the isosurface "voxel" to offset the surface point. Assuming that that
fractional distance can be assigned a number 0-63, I calculate a new compression
ratio of 500:1 instead of 1000:1 with straight 1-byte-per-edge storage. This
changes to about 600:1 if the range can be simplified to 0-7 and these are
stored two values per ascii character -- (probably not worth it to compress that
much). See http://www.stolaf.edu/people/hansonr/jmol/test/proto/ch3cl.jvxl,
which is now about 7400 bytes and includes 0-7 range interpolation data.
A script command describing an orbital might be as long as 4000 characters. My
idea would be to put this in a script file and just call it. Or, maybe we don't
need the inline idea, and we can just load the orbital.
An interesting thing about cube (jvxl) files is that once read, the "orbital"
can be rotated and scaled to any size and any position, so this might just be
the way to express generic hybrid orbitals for display at any atom. A bit of
calculation and some good syntax should, for example, allow:
orbital sp3 1.0 (oxygen and connected(2))
orbital p 0.8 (carbon and connected(3))
(where the number is the scale) all based on a single hardwired (or
user-loaded?) isosurface representing a single tear-drop-shaped orbital lobe.
The idea here would not be to be exact in every detail -- just provide enough of
a surface for depicting the essence of the orbital in a compact format.
Bob
René Kanters wrote:
Hi Bob,
That sounds indeed interesting and promising.
I do seem to recall (it has been a while since I played with the cube
files and my memory isn't very good :-) ), that when I tried to reduce
a cube file to 0s and 1s and set the cutoff at 0.5 (to try to keep the
file size down), the generated surfaces were very angled looking. So I
think (and didn't check) that in the code some kind of interpolation is
done, i.e., the actual values are used to generate a smoother
representation of the data. It looks like you are capturing the result
of this 'pre-processing'.
Personally, I think it is a great idea to implement that.
René
On May 22, 2006, at 12:24 AM, Bob Hanson wrote:
Jmol developers:
I've been thinking tonight about the orbital problem.
What if I told you I could compress CUBE file data for molecular
orbital display with a compression ratio of 1000:1? For example, turn
a 3.7 Mb cube file representing an orbital into a file of about 4K.
Would that be good?
What if I told you we could have "inline" orbitals -- orbitals just
defined right on the script line like this:
isosurfce orbital1 "inline" ...
color $orbital1 red
It's possible! Here's the idea:
Really what an isosurface is either:
1) a bitset -- an n x m x p set of points, each of which is either
the point is or is not within a certain cutoff, or
2) a set of 35-value color indices representing a color of the rainbow.
OK, so for an orbital we have (1), for a mapped charge density plot
or the like, we have (2). Right now I'm focusing on (1), orbitals.
They have just one color.
(We could do two colors as well, but for now, just one.)
I was looking at a cube files and realized that > 99.9% of it is
garbage. Look, we don't need to be transmitting cube files to view
orbitals. All we need are the key "surface" points.
So I propose a new file format. I'll call it JVX for "Jmol Voxel" for
now.
Here is a sample JVX file. (I'm making this up. Bear with me.) The
file is actually just 14 lines and 3630 bytes long. It looks a lot
like a cube file (EXACTLY like a cube file, in fact, so the cube file
reader will read the coordinates).
Title Card Required potential=scf
Electrostatic potential from Total SCF Density
-5 -8.140940 -8.140940 -8.643459
50 0.333333 0.000000 0.000000
50 0.000000 0.333333 0.000000
55 0.000000 0.000000 0.333333
6 6.000000 0.000000 0.000000 -2.130707
1 1.000000 0.000000 1.932284 -2.775380
1 1.000000 1.673407 -0.966142 -2.775380
1 1.000000 -1.673407 -0.966142 -2.775380
17 17.000000 0.000000 0.000000 1.241787
-1 633 0.05
-2 487 0.05
39562 2 52 4 50 5 50 5 51 3 2472 4 50 6 48 7 48 8 47 8 47 7 49 6 51 2
2307 4 49 7 48 8 46 9 46 10 45 10 45 9 47 8 48 6 51 3 2250 6 48 8 46
10 45 10 45 10 45 11 44 11 44 11 45 9 47 8 49 4 2140 3 50 7 47 9 46
10 44 12 43 13 42 18 37 20 36 19 36 19 37 18 38 10 2 2 43 6 2083 3 50
7 47 10 45 11 43 14 41 20 35 22 33 22 34 22 33 22 34 20 35 19 37 17
39 8 47 6 49 4 1922 2 50 8 46 10 45 12 42 21 34 22 33 23 32 24 31 24
32 23 32 23 32 22 34 20 35 18 37 10 45 8 48 6 49 5 1865 7 47 10 44 19
35 22 33 24 31 24 31 25 30 25 30 25 31 24 31 23 32 22 33 21 34 19 36
11 45 8 47 8 48 6 51 1 1758 6 47 16 38 21 34 22 32 24 31 25 30 25 30
26 29 26 29 25 30 25 31 23 32 22 33 20 35 12 43 10 45 9 47 8 48 5
1756 6 48 17 37 20 34 23 31 25 30 25 30 26 29 26 29 26 29 26 29 25 30
25 30 24 31 22 33 19 37 11 44 10 45 9 47 7 51 2 1703 6 47 17 37 21 33
23 31 25 30 26 29 26 29 26 29 26 29 26 29 25 30 25 30 24 31 22 33 20
35 12 44 10 45 9 47 7 50 3 1703 6 47 17 37 21 33 23 31 25 30 26 29 26
29 26 29 26 29 26 29 25 30 25 30 24 31 22 33 20 35 12 44 10 45 9 47 7
50 3 1702 6 48 17 37 20 34 23 31 25 30 25 30 26 29 26 29 26 29 26 29
25 30 25 30 24 31 22 33 19 37 11 44 10 46 8 48 6 51 1 1702 7 47 11 2
3 38 20 35 22 32 24 31 25 30 25 30 25 30 25 30 25 30 25 31 23 32 22
33 20 35 12 43 10 45 9 47 7 49 5 1755 7 47 10 44 19 35 22 33 23 32 24
31 25 30 25 30 25 31 24 31 23 32 22 33 21 34 19 36 11 45 8 47 7 49 5
1756 3 50 8 46 10 45 12 42 20 35 22 33 23 32 24 31 24 32 23 32 22 34
21 34 20 35 18 37 10 46 7 48 6 50 4 1811 3 50 7 47 10 45 11 43 13 42
20 35 21 34 22 34 21 34 21 35 20 36 18 37 16 40 8 47 5 51 2 1923 2 50
7 47 9 46 10 44 12 43 12 43 14 42 18 37 19 37 18 37 17 40 8 48 6 2137
6 48 8 46 9 46 10 45 10 45 10 45 11 44 10 46 9 47 7 51 2 2196 3 51 6
48 8 46 9 46 9 46 9 47 8 47 8 48 6 2360 3 51 6 48 7 48 7 48 7 48 7 49
5 2526 3 52 4 51 4 52 2 39966
47922 3 52 3 52 2 2582 4 51 5 50 5 50 5 51 4 9 1 54 1 2406 3 51 5 49
7 8 1 39 7 6 5 37 7 5 6 38 6 5 7 38 4 6 7 39 2 7 6 50 5 2294 3 51 6 7
3 38 7 5 6 37 8 3 8 36 8 3 8 36 8 2 10 36 7 2 10 37 5 4 8 39 3 5 8 48
6 51 2 2186 3 9 2 40 6 5 6 37 8 3 8 36 20 35 20 35 20 35 20 36 19 36
7 2 10 37 5 4 8 38 4 6 6 40 2 2142 4 7 5 38 6 4 8 36 20 35 20 35 21
34 21 34 21 34 21 35 19 36 8 1 10 36 6 4 8 37 5 7 4 40 3 2088 2 7 6
38 7 3 8 37 19 35 21 34 21 34 14 2 5 34 14 2 5 34 21 34 20 35 20 35 8
3 8 36 7 6 5 38 5 50 4 1990 1 42 2 7 7 37 7 2 10 36 19 35 21 34 14 2
5 34 13 1 2 1 4 34 13 1 2 1 4 34 14 2 5 34 21 34 20 35 8 2 9 36 7 5 6
37 7 49 5 1989 1 42 2 7 7 37 7 2 10 36 19 35 21 34 14 2 5 34 13 1 2 1
4 34 13 1 2 1 4 34 14 2 5 34 21 34 20 35 8 3 8 36 7 5 6 37 7 49 5
2032 2 7 6 38 7 3 8 36 20 35 21 34 21 34 14 2 5 34 14 2 5 34 21 34 20
35 20 35 8 3 8 36 7 6 5 38 5 51 3 2032 4 7 5 38 6 4 8 36 20 35 20 35
20 35 21 34 21 34 20 36 19 36 7 2 10 36 6 5 7 37 5 7 4 40 3 2087 3 51
6 5 6 37 8 3 8 36 20 35 20 35 20 36 19 36 19 36 7 2 10 37 5 4 8 38 4
7 5 2184 3 51 5 8 2 39 7 5 6 37 8 4 7 36 8 3 8 36 8 2 9 37 7 3 8 38 5
4 8 39 3 6 7 49 5 52 1 2186 3 51 5 49 7 48 7 6 4 38 7 6 5 38 6 5 6 39
4 6 6 50 5 50 4 2349 4 51 5 50 5 50 5 51 3 2582 2 53 2 48271
OK, so that's 3630 bytes, and THIS IS ALL THAT IS NEEDED TO DISPLAY
THE TWO SURFACES CONTAINED IN http://www.stolaf.edu/people/hansonr/
jmol/test/proto/ch3cl.cub (3.6 Mb).
The line starting with -1 clues us in that this is NOT a cube file. A
cube file here would have a positive number indicating the number of
surfaces in the file; my number is negative, starting a list of
surfaces in the file, but telling us that this is a JVX file instead.
The other numbers on those two lines are the number of data points
and the cutoffs, but they might be color ranges -- anyway, there's a
line there for some sort of information. What do we need there? We
could discuss that.
That last block of numbers is actually just two separate lines, and
there are no blank lines. See http://www.stolaf.edu/people/hansonr/
jmol/test/proto/ch3cl.jvx
Q: Where did this file come from?
A: The Jmol applet, of course! I just added a few lines to
Isosurface.java, and these numbers appeared on the Java console when
I ran the isosurface script at
file:///C:/temp/jmol/proto/new.htm?model=ch3cl.jvx
For now I just added the header information and clipped it all into a
file by hand. But Jmol could easily create this whole thing.
Q: What does it mean?
A: It's really just TOO simple:
39562 2 52 4 50 5 50 5 51 3 2472 4 50 6 48 7 48 8 47 8 47 ...
says:
"The first 39562 data points are outside the cutoff. The next 2 are
inside, the next 52 are outside, the next 4 are inside, the next 50
are outside..."
Q: What more do we need?
A: You tell me, but I say you could just toss those numbers into a
script and have an isosurface WITHOUT any underlying file:
isosurface mydata1 "inline" {-8.140940 -8.140940 -8.643459} 50
{0.333333 0 0} 50 {0 0.333333 0} 55 {0 0 0.333333} 633 39562 2 52 4
50 5 50 5 51 3 2472 4 50 ...
isosurface mydata2 "inline" {-8.140940 -8.140940 -8.643459} 50
{0.333333 0 0} 50 {0 0.333333 0} 55 {0 0 0.333333} 487 47922 3 52 3
52 2 2582 4 51 5 50 5 50 5 51 4 9 1 54 1 2406 3 51 5 49 7 8 1 39 7 ...
OK, it's a long line for a script. But what of it?
Q: What's the catch?
A: You can't adjust the cutoff. It's going to be *THE* representation
of the surface for that particular web page.
My point is that THAT is all we need. As a web designer you would
first load a cube file into Jmol.jar or the applet and experiment
with a cutoff. Then have Jmol create the .jvx file for you. Maybe
using something like "show isosurfaces" or "getproperty
isosurfaceInfo". Then instead of placing the cube file on the web,
put the .jvx file there, or maybe just create the orbital as an
inline isosurface.
What do you think?
Bob
--
--
Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:[EMAIL PROTECTED]
http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein
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--
--
Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:[EMAIL PROTECTED]
http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein
-------------------------------------------------------
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 v.1.0.1 based on Apache Geronimo
http://sel.as-us.falkag.net/sel?cmd=lnk&kid0709&bid&3057&dat1642
_______________________________________________
Jmol-developers mailing list
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