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
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
Hi Annalisa, The Chimera Multiscale tool makes a low resolution surface for each chain of a PDB model. You could put all of type A surfactant molecules in one chain, and all type B surfactant molecules in another chain. Open the model in Chimera (menu File / Open) then use menu entry Tools / Higher-Order Structure / Multiscale Models, select Multimer type "None" at the bottom of the dialog and press the "Make models" button near the bottom. You'll probably want a higher surface resolution than the default 8 angstroms. Press the Select "All" button at the top of the multiscale dialog, then change the resolution value (middle of dialog) from 8 to 3 and press the Resurface button. By using two PDB chains you will have two surfaces -- one for each type of surfactant. Each can be colored by selecting it (hold ctrl and click on it with mouse button 1), then press the Color button in the multiscale dialog and choose a new color. The multiscale dialog is also able to use matrices to position copies of molecules as Elaine noted. But since your surfactant molecules are all in different conformations I don't think that will help you. Tom
participants (3)
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Annalisa Mercuri -
Elaine Meng -
Thomas Goddard