VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 16 2019 - 09:09:27 CDT

Hi,
  I should also point out that a long time ago a VMD user wrote a
script to parse the BIOMT records in many PDB files and apply the
required transforms to produce the complete biological unit:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/mono2poly/

It could probably be modernized in a number of ways, but it should
still work fine.

Best,
  John

On Mon, Apr 15, 2019 at 10:00:41PM -0700, Ajasja Ljubeti?? wrote:
> You can also download the biological assembly, which has the correct
> oligomerisation state.
> [1]https://www.rcsb.org/3d-view/4V6B/1?preset=symmetry&sele=O
> On Sat, 13 Apr 2019 at 12:07, Vermaas, Joshua <[2]Joshua.Vermaas_at_nrel.gov>
> wrote:
>
> Have you taken a look at the pdb header? The transformation matrices you
> need to generate the biological assembly are usually in the remarks at
> the top, which you can use in conjunction with the move command to make
> the biological assembly. Chimera has a tool that does this automatically
> ([3]https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html).
>
> -Josh
>
>
>
> On 2019-04-12 20:42:59-06:00 [4]owner-vmd-l_at_ks.uiuc.edu wrote:
>
> Dear all,
> I want to visualise the spherical structure of ferritin ( homo 24 -
> mer ) in VMD. The pdb file contains only a monomer.
> How can I make to get the whole sphere in VMD ?
> Thank you !
>
> References
>
> Visible links
> 1. https://www.rcsb.org/3d-view/4V6B/1?preset=symmetry&sele=O
> 2. mailto:Joshua.Vermaas_at_nrel.gov
> 3. https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html
> 4. mailto:owner-vmd-l_at_ks.uiuc.edu 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/