[PyMOL] rebuilding icosohedral virus structure - symexp?

[Dr. D. J. W. P. <da...@ch...>]

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=20=

complete protein spherical capsid structure.

can I use pymol
symexp command to do this?

I tried loading the file then doing
symexp sym=3D1ch8h,(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=20=

capsid structure as a file that Bodil reads properly. Pymol of course=20
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=20=

hand 1 by 1 in SwissPDBviewer (and the linux version is a bit funny...i=20=

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 Jyv=E4skyl=E4
Jyv=E4skyl=E4 FIN 40014
Finland
+358 (0)14 260 4183 (work)
+358 (0)414740463 (mob)

http://www.chalkie.org.uk
da...@ch...
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