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 pymol
symexp command to do this?
I tried loading the file then doing
symexp sym=1ch8h,(1ch8h),20
but nothing seemed to happen?
I'm doing it wrong i'm sure.....
I did manage to do this in SwissPDBViewer, but I cant save the complete
capsid structure as a file that Bodil reads properly. Pymol of course
reads the file ok....... So suppose it is a bodil problem...
anyway, can i use symexp to do this automatically. you have to do it by
hand 1 by 1 in SwissPDBviewer (and the linux version is a bit funny...i
did it on a mac)
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 (0)14 260 4183 (work)
+358 (0)414740463 (mob)
http://www.chalkie.org.uk
d...@chalkie.org.uk
wh...@cc.jyu.fi
