VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Apr 05 2004 - 14:11:45 CDT

Hi,
  Try using something like this (replacing the upper left 3x3 matrix elements
as appropriate of course):

set sel [atomselect top "all"]
$sel move {{1.0 0.0 0.0 0.0}
           {0.0 1.0 0.0 0.0}
           {0.0 0.0 1.0 0.0}
           {0.0 0.0 0.0 1.0}}
$sel writepdb /tmp/myfile.pdb

While it would be great to automatically parse PDB files and read
these transformation matrices in a script, as far as I know there is
not standard method of storing them. The transformation matrices
are just included in the comments section of the file and don't have
any guaranteed formatting or ordering to my knowledge. If someone knows
otherwise however, and they can supply a spec, it would be fairly simple
to write a Tcl script that does this automatically if formatting is
known and guaranteeably consistent.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Apr 05, 2004 at 06:35:06PM +0300, Dr. Daniel James White PhD wrote:
> Hi,
>
> I have a virus envelope protein structure pdb entry,
> and I want to rebuild the whole virus protein shell
> using the symmetry transformations given in the 180 (60 trimers)
>
> REMARK 350 BIOMT1 1 1.00000 0.00000 0.00000
> REMARK 350 BIOMT2 1 0.00000 1.00000 0.00000
> REMARK 350 BIOMT3 1 0.00000 0.00000 1.00000
> REMARK 350 BIOMT1 2 0.80900 0.30900 0.50000
> REMARK 350 BIOMT2 2 etc...
> REMARK 350 BIOMT3 2 etc...
> etc......
>
> lines of the pdb file. These lines give the transformations to give the
> complete protein spherical capsid structure.
>
> can I use some vmd
> command to do this?
>
> I did manage to do this in SwissPDBViewer, but it is very boring doing
> it 1 by 1 and I cant save the complete capsid structure as a file that
> Bodil reads properly.
>
> can vmd do this,
> if not, anyone know how I can?
>
> cheers
>
> Dan
>
> Dr. Daniel James White BSc. (Hons.) PhD
> Cell Biology
> Department of biological and environmental science
> PO Box 35
> University of Jyväskylä
> Jyväskylä FIN 40014
> Finland
> +358 14 260 4183 (work)
> +358 468102840 (new mobile)
> NEW PHONE NUMBER!!!
>
> http://www.chalkie.org.uk
> dan_at_chalkie.org.uk
> white_at_cc.jyu.fi 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078