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

Karel W. F. de Pourcq karelw.f.depourcq at e-campus.uab.cat
Tue Aug 9 16:46:52 PDT 2016

Dear Tom, Eric and Elaine:

Sorry to answer so late to your replies, I missed them until now!

As a recap, the problem proposed was to generate a sphere, and to cover it
with a high number of "molecular arms" which would grow from the sphere
surface to the outside.

The solution I found was to:
a) Create the sphere which I wanted to cover with "n" molecule chains.
b) Open one copy of the desired molecule, in the desired position
simulating its "binding" on the sphere surface.
c) Open an additional copy of the molecule, and rotate this molecule 180º
around the sphere surface (i.e. putting the center of rotation aroun the
sphere with "cofr" command), with the "turn" command.
d) Save the two molecules (rotated and unrotated) as only one .pdb.
e) Close the single copies of the molecule and open the newly created .pdb
file, two times (hence obtaining 4 molecules on the surface). One of these
copies is re-distributed as desired, with the "turn" command. Save these as
one single .pdb.
f) Close the open molecules (except the sphere), and newly open two copies
of the previous .pdb file. Move one of them as required, and save as a
single .pdb. And so on and so forth.
g) Repeating this process as required, the sphere is quickly covered by the
molecules as intended, in a quite orderly way, if using the appropriate
"turn" commands. The number of arms grows exponentially.

Neverthless I will try out the solutions you propose, as I have to repeat
part of the job, and I want to give Chimera some more practice. Thanks a
lot, and my apologies for my late reaction.

Kind greetings from Barcelona, Spain,


2016-07-13 20:46 GMT+02:00 Tom Goddard <goddard at sonic.net>:

> Another approach is to use the Chimera Cage Builder tool (menu Tools /
> Higher-Order Structure) and place copies of a molecule at pentagon and
> hexagon faces using the sym command.  Here’s a picture where I did this
> with 80 copies influenza hemaglutinin 5huf using sym command
> sym #1 group #0,p6
> after building the cage by hand and placing one copy of 5huf on a hexamer
> — about 10 minutes work.
> Tom
> On Jul 13, 2016, at 11:10 AM, Eric Pettersen  wrote:
> You would have to do a bunch of (fairly straightforward) math yourself,
> but you can do this basically with a bunch of ‘turn’ commands.  Let’s say
> your structure naturally lies on the X axis and that you want to arrange N
> copies around your sphere.  Open N copies, and translate them along X
> (using the ‘move’ command) to put the end you want at the sphere radius and
> the rest outside the sphere.  For each copy use a ’turn’ command specifying
> the center and Y axis to position the copy in the right direction in the XZ
> plane, then a second turn command to raise or lower it to its final
> position on the sphere.  You will have to do some math to compute the axis
> for the second turn command:  the axis will be in the XZ plane and
>  perpendicular to the vector from the sphere center to the post-first-turn
> position of the structure (i.e. where the Z axis would be if the first turn
> had been applied to it).
> —Eric
> Eric Pettersen
> UCSF Computer Graphics Lab
> On Jul 13, 2016, at 10:50 AM, Elaine Meng > wrote:
> 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  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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