A scene I've been wanting to remake ever since I made it in grad school - alas,
that HDD is long gone.

Coordinate data from a pdb file.
Trimmed and processed in OpenOffice Calc
Atom bonding done (painfully) by hand

1400 lines of code.

The double helix is neither straight up, nor centered on the y-axis. <eyeroll>
_Thanks_ science guys...

I have a small pile of pdf's concerning how to fit a parametric equation to a
helix.

It would be nice to:
Straighten the thing up
Find the exact center / axis of the double helix
Have macros and modular pieces to assemble the sugar-phosphate backbone and
nucleotide base pairs in long chains and splines

I'm thinking about looking at TOK's "map any triangle to any other triangle"
macro to figure out the rotation, flip, and positioning of the subunits, such
that the sense and antisense strands can be aligned.

I haven't yet had the intestinal fortitude to try and blob this yet.

Now it's time for dinner, and an exciting night of sorting 300-page incoming
freight orders.

- BW

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Attachments:
Download 'b-dna.png' (193 KB)

Preview of image 'b-dna.png'

hi,

"Bald Eagle" <cre### [at] netscapenet> wrote:
> A scene I've been wanting to remake ever since I made it in grad school - alas,
> that HDD is long gone.
>
> Coordinate data from a pdb file.
> Trimmed and processed in OpenOffice Calc
> Atom bonding done (painfully) by hand
>
> 1400 lines of code.
> ...

not too sure about the choice of colours and lighting, but .. wow.  v cool.



@TdG 'Roman Dodecahedron'.

also v cool.  has me wonder, did it have a function, or was it just "decor" ?


regards, jr.

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Op 30/01/2024 om 19:54 schreef jr:
> hi,
> 
> "Bald Eagle" <cre### [at] netscapenet> wrote:
>> A scene I've been wanting to remake ever since I made it in grad school - alas,
>> that HDD is long gone.
>>
>> Coordinate data from a pdb file.
>> Trimmed and processed in OpenOffice Calc
>> Atom bonding done (painfully) by hand
>>
>> 1400 lines of code.
>> ...
> 
> not too sure about the choice of colours and lighting, but .. wow.  v cool.
> 
I certainly agree also about the wow, and I admire the task you have 
achieved. Strange indeed that location and orientation were away from 
the origin. I cannot imagine how the original builders could have 
achieved that...

> 
> 
> @TdG 'Roman Dodecahedron'.
> 
> also v cool.  has me wonder, did it have a function, or was it just "decor" ?
> 
Unknown. Read the wikipedia page attached ;-)

-- 
Thomas

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Thomas de Groot <tho### [at] degrootorg> wrote:


> > not too sure about the choice of colours and lighting, but .. wow.  v cool.
> >
> I certainly agree also about the wow, and I admire the task you have
> achieved. Strange indeed that location and orientation were away from
> the origin. I cannot imagine how the original builders could have
> achieved that...

X-ray crystallography.
And they probably didn't care because they likely have taxpayer purchased
software packages that will parse, assemble, and orient it with a few clicks.

I currently have my nose to the ground, trying to find an algorithm to generate
the inverse of a 9x9 rigid body transform matrix - if I can puzzle that out,
then any object specified with 4 points can be mapped to any other instance with
a transform {matrix{}} statement.
Then I can take one base, look over where it sits somewhere else in the helix,
and calculate exactly how to get it from one place to another.

> > @TdG 'Roman Dodecahedron'.
> >
> > also v cool.  has me wonder, did it have a function, or was it just "decor" ?
> >
> Unknown. Read the wikipedia page attached ;-)

I only read that one page - but it occurred to me that with the different sized
holes and 12 sides, that maybe it some sort of monthly calendar.  If all the
holes were unique sizes you could drop a graduated cone into a hole, and it
would sink down to a unique depth.   But that probably not at all what it was
used for.  :D

- BW

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On 2024-01-30 14:54 (-4), jr wrote:
> 
> not too sure about the choice of colours and lighting, but .. wow.  v cool.

Traditional colors:
  Hydrogen - white
  Carbon - black, or sometimes gray
  Nitrogen - blue
  Oxygen - red
  Phosphorus - orange, or sometimes purple

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Op 31/01/2024 om 12:27 schreef Bald Eagle:
> Thomas de Groot <tho### [at] degrootorg> wrote:
> 
> 
>>> not too sure about the choice of colours and lighting, but .. wow.  v cool.
>>>
>> I certainly agree also about the wow, and I admire the task you have
>> achieved. Strange indeed that location and orientation were away from
>> the origin. I cannot imagine how the original builders could have
>> achieved that...
> 
> X-ray crystallography.
> And they probably didn't care because they likely have taxpayer purchased
> software packages that will parse, assemble, and orient it with a few clicks.
> 
> I currently have my nose to the ground, trying to find an algorithm to generate
> the inverse of a 9x9 rigid body transform matrix - if I can puzzle that out,
> then any object specified with 4 points can be mapped to any other instance with
> a transform {matrix{}} statement.
> Then I can take one base, look over where it sits somewhere else in the helix,
> and calculate exactly how to get it from one place to another.
> 
That could be very useful. Also in a universal sense, applied to all 
sort of transformations/mutations.

>>> @TdG 'Roman Dodecahedron'.
>>>
>>> also v cool.  has me wonder, did it have a function, or was it just "decor" ?
>>>
>> Unknown. Read the wikipedia page attached ;-)
> 
> I only read that one page - but it occurred to me that with the different sized
> holes and 12 sides, that maybe it some sort of monthly calendar.  If all the
> holes were unique sizes you could drop a graduated cone into a hole, and it
> would sink down to a unique depth.   But that probably not at all what it was
> used for.  :D
> 
Who knows. At the moment, the context of the finds is ambiguous. It 
certainly was a highly prised object (included within hoards for 
instance), not much physically manipulated (few wear traces). A 
ritualistic purpose seems indicated. Also, restricted to the NW part of 
the Roman empire: Gaul and the British Isles.

-- 
Thomas

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hi,

> > also v cool.  has me wonder, did it have a function, or was it just "decor" ?
> Unknown. Read the wikipedia page attached ;-)

did that before posting, just saw a listing of some TV series episodes, by
"series".  (and since I do not own a "tellie", nor watch, my eyes must have
"glazed over" :-))


@Cousin Ricky: "Traditional colors"

thanks for the explanation.  (my chemistry is right up there with my maths
</grin>. still think it "too dark", somewhat :-).  maybe BE can/will post an
animation where the molecule rotates (to get a better view))


regards, jr.

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Op 1-2-2024 om 08:28 schreef jr:
> hi,
> 
>>> also v cool.  has me wonder, did it have a function, or was it just "decor" ?
>> Unknown. Read the wikipedia page attached ;-)
> 
> did that before posting, just saw a listing of some TV series episodes, by
> "series".  (and since I do not own a "tellie", nor watch, my eyes must have
> "glazed over" :-))
> 
Oh, sorry! yes, that page was meant as a context. I referred above to 
the second wiki page I added, about the dodecahedron proper. I am highly 
interested in archaeology, so I try to follow the different developments 
and finds. This one was particularly intriguing as - until now - it is 
completely unknown what the object represented or was used for, or in 
what context, religious or other. The finds are restricted to the Roman 
parts of Gaul and the British Isles, so possibly a link with (non-Roman) 
Gallic believes can be inferred...

-- 
Thomas

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Thomas de Groot <tho### [at] degrootorg> wrote:

"A ritualistic purpose seems indicated."

"it is completely unknown what the object represented or was used for, or in
> what context, religious or other."

I always find these ritual/religious explanations tiresome - Look around the
modern world, and try to even count the number of knick-knacks, baubles,
bric-a-brac, curios, ornaments, souvenirs, and trinkets people buy and
accumulate - all of which have zero ritualistic or religious purpose or meaning.

It could have been a _designer_ dodecahedron that was very trendy, and only the
wealthiest could afford then, to flaunt their status.

If it was found with hordes, maybe the holes were used to measure coins to
detect coin-shaving.  I have solid state electronic scales and an electronic
device to test the purity and composition of gold and silver alloys.  None of
which make any sense to a future civilization once the batteries were long gone.
Granted, the alloy tester is $1000, but the scale is a cheapo mass-market thing
that has no real inherent value, but is only used in proximity to coins, etc.

Maybe it was tabletop sign, to indicate membership in a trade guild.

Maybe it was a tip jar.  :D

It could be an ancient "Challenge Coin" and the holes were to hold shotglasses.
Maybe it held incense or pencils or quills.

Perhaps it's a loupe, and the glass lenses are long gone.  The knobs at the
vertices held the device the proper distance from the surface being observed.

Maybe it's a 12-sided die, and was used for gambling.

Maybe it was used by scammers to do zodiac astrological fortune telling.

Perhaps it held an oil lamp, either for illumination, or as a distant forerunner
of the USB coffee mug heater.  Or a camp stove.

Maybe it's a mandrel or a template for assembling something - perhaps with cord,
and the holes are for aligning the loops of the developing knots.

It could be a neckerchief slide or similar fastening device.

Has anyone blown into it?  Maybe it's a whistle.




Perhaps we can only know its true purpose once it's been rendered sufficiently.

CSG-Dodecahedron challenge!  Now for a cool Roman render rig as a backdrop!

- BW

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Thomas de Groot <tho### [at] degrootorg> wrote:
> > did that before posting, ...
> Oh, sorry! yes, that page was meant as a context.

no worries.  looks like I missed the second link you provided.


> ... I am highly interested in archaeology, ...

no kidding.  first the vase, now this..  </grin>

and that Wikipedia article disappointed a little in that there are no measures
attached; _now_, of course, I've tons of questions.  for instance, I'd like to
know whether the circular openings are of the same sizes across unrelated finds,
whether they appear to be in "straight" ratios to one another, etc, etc. strange
that all of these museum items seem not even to have been looked at for
"scientific study".


regards, jr.

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