VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Apr 05 2016 - 11:05:11 CDT

Ahh! Thanks for the link to the PDB. For proteins, the PDB header
actually gives you the information you need to do the rotations needed
for the biological assembly. Look for the lines like this at the top of
the pdb:

REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000

Those give you the rotation + translation matrix you need for the first
two copies of the chain, which you can put together with something like
this:

mol new 1AEW
#First one doesn't move
mol new 1AEW
#Second one does.
set all [atomselect top "all"]
$all set chain B ; #Rechain this one. Makes it easier later.
$all move [list [list -1 0 0 0] [list 0 -1 0 0] [list 0 0 1 0] [list 0 0
0 1]] ;#To make the translation matrix 4x4, a 0 0 0 1 row is always
added to the end.
#Do the other 22 copies here
#Merge them all together
|set mol [::TopoTools::mergemols [molinfo list]]
#Write out the new molecule
animate write pdb merged.pdb $mol

I think Chimera has a tool to do this automatically, but in the past
I've always just done it this way.

-Josh
|

On 04/05/2016 10:23 AM, Olya Kravchenko wrote:
> Hi Josh,
>
> thanks for replying. If I were to construct an octahedral structure
> such as this in VMD/NAMD:
> http://www.rcsb.org/pdb/explore/explore.do?structureId=1AEW 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
> approach?
>
> Olga
>
> On Mon, Apr 4, 2016 at 6:06 PM, Josh Vermaas <vermaas2_at_illinois.edu> 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
>>>