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
<sunyep...@yahoo.com.cn<mailto:sunyep...@yahoo.com.cn>> 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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