Ok, biological unit, thats great!
but now,
how do I save this virus capsid as a a pdb or mol file
where each of the many subunits have a different chain identifier.
When I save the virus caspid structure with all subunits visible, the
pdb file still only has on subunit in it, not all of them...
I want to open it in Bodil (or Pymol or whatever) and only view the
chains I want to see.
I just want to see the subunits around one of the 5 fold symmetry axes,
ie with the 5 fold axis in the middle surrounded by the 5
trimers/triangles that surround the 5 fold axis.
cheers
Dan
On 2 Apr 2004, at 17:57, Todd Geders wrote:
I've found the easiest way to do this under PyMOL is to download the
"Biological Unit" version of the PDB file. They've already regenerated
the virus particle for you. It will only show one of the particles at
a
time unless you check Movie->Show All States.
~Todd Geders
On Fri, 2004-04-02 at 07:14, 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 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
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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
