From: Olya Kravchenko (
Date: Tue Apr 05 2016 - 10:23:46 CDT

Hi Josh,

thanks for replying. If I were to construct an octahedral structure
such as this in VMD/NAMD: out of one
chain that is provided, where would I start?

My question was more general though - say I want to construct a
spherical molecule, that is empty inside, and maybe this structure is
large enough that placing each chain by hand is not optimal, and there
are several centres of symmetry (i.e. Fibonacci lattice isn't
applicable?). It would be convenient to have a spherical surface of a
given diameter that can be used for distributing residues and then one
can remove the surface and equilibrate what's left. Is there another


On Mon, Apr 4, 2016 at 6:06 PM, Josh Vermaas <> wrote:
> Hi Olga,
> Could you be a bit more specific? I happen to have recently acquired some
> experience in generating large spheres of repeated molecules. What I found
> to be the most difficult was generating approximately uniform points on the
> spherical surface (which I solved by looking into Fibonacci Spheres, which
> are approximately uniform for large enough N). From there, each molecule
> needs to be reoriented so that it is pointing the right (or in a random)
> direction.
> I don't think VMD has an automatic tool to do this, but conceptually its a
> straightforward problem in scripting, which I encourage you to pursue.
> -Josh Vermaas
> On 04/04/2016 03:16 PM, Olya Kravchenko wrote:
>> Hi all,
>> I wonder if anyone has experience constructing a spherical molecule
>> starting with one chain? I have the complete spherical structure
>> already, but it was inherited and I'd like to learn how to construct
>> one myself.
>> All I can think of is just manually put it together chain by chain
>> (should be 24 chains). Are there any automatic tools for such a task?
>> Something that would create spherical symmetry?
>> Thanks in advance!
>> Olga