[Chimera-users] placing copies of a molecule to cover a sphere

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 13 10:50:26 PDT 2016


Hi Karel,
Looks like an interesting project!

There isn’t a feature in Chimera to automatically cover the surface of a sphere with copies of some other structure. There is a “sym” command to create symmetrically placed copies of a molecule, but you would need to specify in the command the type of symmetry, the center, and (if applicable) the axis.  The symmetries about a center only go up to icosahedral, so as I understand it, you could only end up with 20 copies of the starting structure (although I suppose that starting structure could have more than one of your molecules, or maybe there could be an iterative process building up to higher multimers).
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>

You may need to use another program (custom script written yourself or maybe tools available in some other package) to determine how many copies cover the sphere at the appropriate density, and then the transformations to place the copies.  I wonder if something like CellPack is the appropriate tool, but I don’t know how to use it myself.
<http://www.cellpack.org/>

There is also a micelle builder in CHARMM-GUI but I realize that may not be exactly what you want either.
<http://www.charmm-gui.org/?doc=input/micelle>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 13, 2016, at 9:43 AM, Karel W. F. de Pourcq <karelw.f.depourcq at e-campus.uab.cat> wrote:

> Dear Chimera team:
> 
> I am a student of a Msc. in Bioinformatics at the Autonomous University of Barcelona. I am using Chimera to prepare visual representations of molecular events, and I write in order to ask if there is a straightforward way in which to:
> 
> a) Create a sphere of a certain diameter:
> Yes, I found how to do it already: with the "shape" command. This is solved.
> 
> b) In an orderly and distributed way, cover that sphere with a number of copies of a molecule chain, anchored over the sphere's surface by one of their ends (and the other end of the molecule protruding towards the outside).
> I believe I could do it manually for a small system. Is there some kind or automated and more convenient way to do this for a large sphere, linking its surface with hundreds of molecules of -for instance- dodecane? I could not find explicitly a way to do something similar to what I am trying to do.
> 
> I attach an image of a 2-d representation of something similar to what I would like to represent. The difference is that I would like to cover the surface.
> 
> <Sphere_and_molecules.png>
> 
> I thank you a lot in advance for your time.
> Kind greetings from Barcelona, Spain,
> 
> Karel De Pourcq




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