Computer Visualization in Avogadro

I’ve been asked to give a talk in February about Avogadro and chemical
visualization. My colleague wanted a one paragraph description of the
sort of problems we’re trying to solve. In other words, what would be
good projects for first-year graduate students in scientific
visualization.

Now I have a few ideas myself, but I’m curious to hear from others.
What types of problems are we trying to solve with Avogadro? What are
some good visualization projects over the next few months?

Cheers,
-Geoff

To make this clear, I’m not looking for technical ideas (e.g., use
impostors and GLSL to get cooler shadows).

I’m looking for the key ideas. What makes Avogadro more intuitive than
something else. Screencasts are good. Saying that we want to adapt
this idea in a drawing or painting desktop program for chemical 3D
visualization is good.

-Geoff

On Dec 20, 2007, at 3:44 AM, Carsten Niehaus wrote:

Now I have a few ideas myself, but I’m curious to hear from others.
What types of problems are we trying to solve with Avogadro? What are
some good visualization projects over the next few months?

Hey!

Are you looking for technical ideas (as “this and that OpenGL-
thingy”) or for features we would like to have in Avogadro?

I have quite some ideas (taken from other application I am using
(having to use) in school). I could make screencasts of them (in
case there is a way to record my desktop in windows?).

As I don’t know OpenGL I cannot give technical hints, just ideas of
what a teacher would like to have…

On Dec 20, 2007, at 3:44 AM, Carsten Niehaus wrote:

I have quite some ideas (taken from other application I am using
(having to use) in school). I could make screencasts of them (in
case there is a way to record my desktop in windows?).

To give you some idea of what I’m thinking. I’m going to talk about
the difficulty in having live, useful information displayed when
"action" is occurring. This is along the idea of what the bond-centric
manipulation tool does – show bond lengths, angles, etc.

  • What if I’m drawing, and it shows me the bond length as I draw?
  • What if I’m drawing, and it shows me live updates of chiral atoms
    and stereochemistry.[1]
  • What if I use the manipulate tool and it shows me bonds and angles
    for “close contacts?” or the angle between the new position and the
    old one?
  • What if I use the h-bond engine and it shows me the hydrogen-bonding
    distance when a new h-bond is “formed.” Sounds great for molecular
    dynamics simulations!
  • What if I had a “steric repulsion” engine which would show non-
    bonded contact between two atoms?
  • What if we had a manual text annotation tool?
  • What if we could add measurements that would automatically update
    during a reaction movie?
  • What if we had a “timeline” view for reactions or molecular
    vibrations or molecular dynamics?

This is a chance that we can ask “what if I had a chemistry tool that
worked like this” rather than focusing on the specific questions of
writing code. I think this is a great opportunity to dream about how
Avogadro might work – and what are goals are.

Hope that helps a bit.
-Geoff

[1] ChemPad: http://graphics.cs.brown.edu/research/chempad/report.pdf
See the second page, for example, where it automatically tests CIP
naming.

Here are some docking/drug design based ideas:

  • make a surface for the ligand and binding pocket --> detect emty
    space and give some valuable parameters which would help determine how
    to fill the space with an extention to the ligand (volume,
    lipophylicity, charge, …)
  • isolate the binding site surface and allow the user to edit the
    ligand inside it, when you place atoms outside the binding site, the
    atoms and bonds will be colored red (this would be really nice if we
    just hide the binding site, and run AutoOpt while editing the ligand)
  • we could also color the binding site surface green or red for
    favourable and unfavourable interactions
  • display pharmacophores inside these binding site surfaces, or allow
    the user to create pharmacophores inside a binding site (requires
    visuable residues), the pharmacophores could be displayed as wireframe
    spheres with a color for different interaction points (HBD, HBA, +/-
    charge, lipophilic substituent, …)

Tim

On Dec 20, 2007 2:43 PM, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:

On Dec 20, 2007, at 3:44 AM, Carsten Niehaus wrote:

I have quite some ideas (taken from other application I am using
(having to use) in school). I could make screencasts of them (in
case there is a way to record my desktop in windows?).

To give you some idea of what I’m thinking. I’m going to talk about
the difficulty in having live, useful information displayed when
"action" is occurring. This is along the idea of what the bond-centric
manipulation tool does – show bond lengths, angles, etc.

  • What if I’m drawing, and it shows me the bond length as I draw?
  • What if I’m drawing, and it shows me live updates of chiral atoms
    and stereochemistry.[1]
  • What if I use the manipulate tool and it shows me bonds and angles
    for “close contacts?” or the angle between the new position and the
    old one?
  • What if I use the h-bond engine and it shows me the hydrogen-bonding
    distance when a new h-bond is “formed.” Sounds great for molecular
    dynamics simulations!
  • What if I had a “steric repulsion” engine which would show non-
    bonded contact between two atoms?
  • What if we had a manual text annotation tool?
  • What if we could add measurements that would automatically update
    during a reaction movie?
  • What if we had a “timeline” view for reactions or molecular
    vibrations or molecular dynamics?

This is a chance that we can ask “what if I had a chemistry tool that
worked like this” rather than focusing on the specific questions of
writing code. I think this is a great opportunity to dream about how
Avogadro might work – and what are goals are.

Hope that helps a bit.
-Geoff

[1] ChemPad: http://graphics.cs.brown.edu/research/chempad/report.pdf
See the second page, for example, where it automatically tests CIP
naming.


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