Re: [PyMOL] symmetry operation to generate the whole virus particle

[Troels E. L. <tl...@gm...>]

You are probably looking for this:

http://pymolwiki.org/index.php/Symexp

Or else you can do it in CCP4.
Coordinate utilities -> Edit PDB file ->Use pdbset -> generate chains via
symmetry operations

Troels Emtekær Linnet
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2013/2/28 yp sun <sun...@ya...>

> Dear pymol users:
>
> Usually pymol can show only one chain when you open a pdb file of virus
> particles (such as 2buk,1sva, etc.). I am trying to create the whole virus
> particle and I know it may need applying symmetry operations. And these
> symmetry operation has been given in the pdb files. For example, the follow
> is the symmetry operation of 2buk:
>
> REMARK
> 350
> REMARK 350 GENERATING THE
> BIOMOLECULE
> REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE
> KNOWN
> REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF
> THE
> REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT
> TRANSFORMATIONS
> REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC
> AND
> REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE
> GIVEN.
> REMARK
> 350
>
> But I don't understand how to do symmetry operations. Can pymol do these
> or other software is needed? Please help.
>
> Yeping Sun
> CAS Key Laboratory of Pathogenic Microbiology & Immunology
> INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES
> NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china
>
>
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