VMD-L Mailing List

From: Dr. Daniel James White PhD (dan_at_chalkie.org.uk)
Date: Mon Apr 05 2004 - 10:35:06 CDT

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