Growing a Molecule?

[Tom]

Rob-

I came across a puzzle that you might help with. I am trying to "grow" a molecule, segment by segment, almost like a time lapse thing, but I can't figure out how to control the slow growth of each segment using pose sliders.

Maybe there is a smarter way...see you at noon.

Tom

Molecule.mdl

[robcat2075]

Here is the result of today's efforts. Thanks for posing the question, Tom!

PRJ:

MoleculeGrowing006 GrowingStick.prj

Render Preset:

MoleGrow.pre

Animation:

 

[KingVidiot]

nice idea, sorry I missed the session - I was up super late working on stuff and woke up at noon

I was building molecular models from scratch back in AM 99 (7.1) using PDB files and RasMol as references, since I'm a bio/chem nerd - my degree was in Cell and Molecular Biology

the tricky thing abut this design is to be chemically accurate you need to make each atom a diff size and color (all N red, all O blue, all H gray or white, etc.) based on the element, just like PDB files and following the IUPAC standard
that was a big part of the grunt work as I worked on models of caffeine and its brother theobromine (chocolate), among other structures

[robcat2075]

The archive video replay is up now.

 

5 hours ago, KingVidiot said:

...the tricky thing about this design is to be chemically accurate you need to make each atom a diff size and color (all N red, all O blue, all H gray or white, etc.) based on the element..

I think we could incorporate that into Pose settings so we could still use one model for each atom.

You could make an ON/OFF Pose for each element that sets the size and color... or you could put them all on the continuum of one Pose slider.

[Tom]

cool!

[KingVidiot]

could be a fun thing to try
the other issue is the geometry of the molecule based in the atoms 

as you change out atoms the geometry needs to change (angles and distances) due to neigbor layout and the types of bonds (ionic, covalent, Hydrogen bonding) and as a structure gets more complicated like amino acids forming proteins or DNA/RNA the structure (primary, secondary, tertiary...) can change drastically based in attraction like H-bonding or van der Waals forces  

this get pretty nerdy but it's important if you are going to submit to a science site, publication, teacher, student, or other related person or contest

otherwise basic diagrammatic stuff works OK

now you can see why I was working on ways to build structures in AM many years ago and got distracted on other stuff, lots of stuff to consider, especially based on what I was going to do with the material - RasMol was a lot easier and completely accurate, but less customizable

good stuff here nonetheless - nice to see it

I was going to make a Covid-19 viroid but opted for a nice OBJ made by someone online and pretty cheap - I can still use it as a prop in AM