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

[Sampson, J. <Jar...@ny...>]

Hi Yeping -

Try using:

fetch 2buk, type=pdb1, multiplex=1, async=0

This will fetch the biological assembly (type=pdb1) from the pdb, split the 60 states into separate objects (multiplex=1), and tell PyMOL to wait for all this to be completed before moving to the next command in a .pml script (async=0).

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
Old Public Health Building, Room 610
341 East 25th Street
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/




On Feb 28, 2013, at 4:30 AM, yp sun <sun...@ya...<mailto:sun...@ya...>> wrote:

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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