Hi Ezra,
Capsid was a typo, I ment to say the matrix of the virus. The pdb1 file is a
trimer of the protein. I now how the trimeric form of the protein interacts to
form the matrix and was hoping that a script could help me build the complete
matrix sphere.
Marcelo
> On Apr 17, 2015, at 4:53 AM, Ezra Peisach <ezra.peisach+py...@rcsb.org> wrote:
>
> The full biological unit should be available in biological assembly file.
> Have you tried using the fetch command?
>
> i.e.:
>
> fetch 1avd, type=pdb1
> set all_states, on
>
>
> The first retrieves BA #1, the all_states shows the models.
>
> If there is something wrong with the assembly file - then by all means
> contact the PDB...
>
> Ezra
>
>
> On Fri, Apr 17, 2015 at 1:34 AM, Marcelo Marcet <mmar...@nait.ca
> <mailto:mmar...@nait.ca>> wrote:
> Hi Everyone,
>
> I have been trying to build a virus capsid using pymol. The biological unit
> for the complete structure is not available. :(
>
> My first attempt at getting this done was by using the “rotate” and
> “translate” commands. Unfortunately, these commands can only move objects
> either relative to the main axes or the viewer’s position (not relative to
> existing objects), thus I had to calculate the rotation angles and
> translation angle/distances for every single object (not practical).
>
> I have been advised to try the ‘supercell.py’ script. Is supercell the right
> tool for the job? Any advice would be much appreciated.
>
> Marcelo
>
>
>
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