[Chimera-users] Surfactant

[Elaine Meng]

Hi Annalisa,
Chimera (at least currently) does not have much building ability or  
features for solvating structures or constructing assemblies such as  
micelles.

To show a micelle with Multiscale Models in Chimera, you would need:
(a) coordinates for a minimal repeating unit in the "micelle" (each  
molecule a separate chain)
(b) matrices describing the symmetry operations to apply to those  
coordinates to construct the whole "micelle"

Look at the contents of your virus PDB input as an example.  You  
would need to know the size of the desired micelle in order to create  
the symmetry operators.  Actually, this "micelle" would be an  
approximation only, because as I understand it, micelles are  
disordered as opposed to the symmetrical construct you would obtain  
with the information above.  Another approach is to use some other  
program to build the micelle and read it into Chimera.  Multiscale  
Models would show a separate "blob" for each chain in the input (i.e.  
give a different chain ID to each thing you want to be a separate blob).

My best guess is that molecular mechanics/molecular dynamics programs  
may have micelle-building capabilities.  I recommend looking at  
papers that involve atomistic models of micelles and looking at their  
"materials and methods" sections to see how others have constructed  
such models.
Best,
Elaine

On Aug 14, 2006, at 4:31 AM, Annalisa Mercuri wrote:

> Hallo everybody,
>
> I'm working with surfactants and emulsions. I'd like to use Chimera to
> reconstruct a micelle with my components, but I have no clue how to do
> that. Further my emulsion is made by a mixture of two surfactants.  
> I would
> like to have a emulsion droplet image like the virus one. What do you
> suggest?
>
> Thank you for your help and advices
>
>
> Annalisa Mercuri MSc
> PhD Student
> School of Chemical Sciences and Pharmacy
> University of East Anglia
> Norwich
> Norfolk
> NR4 7TJ
> UK

-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html