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@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