3356–3358
Nucleic Acids Research, 2003, Vol. 31, No. 13
DOI: 10.1093/nar/gkg587
SEM (Symmetry Equivalent Molecules): a web-based
GUI to generate and visualize the macromolecules
A. S. Z. Hussain, Ch. Kiran Kumar, C. K. Rajesh, S. S. Sheik and K. Sekar*
Bioinformatics Centre, Supercomputer Education and Research Centre, Indian Institute of Science,
Bangalore, 560 012, India
Received December 30, 2002; Revised and Accepted April 9, 2003
ABSTRACT
SEM, Symmetry Equivalent Molecules, is a webbased graphical user interface to generate and
visualize the symmetry equivalent molecules (proteins and nucleic acids). In addition, the program
allows the users to save the three-dimensional atomic
coordinates of the symmetry equivalent molecules in
the local machine. The widely recognized graphics
program RasMol has been deployed to visualize the
reference (input atomic coordinates) and the symmetry equivalent molecules. This program is written
using CGI/Perl scripts and has been interfaced with all
the three-dimensional structures (solved using X-ray
crystallography) available in the Protein Data Bank.
The program, SEM, can be accessed over the World
Wide Web interface at http://dicsoft2.physics.iisc.
ernet.in/sem/ or http://144.16.71.11/sem/.
INTRODUCTION
In the present structural Bioinformatics era, advanced tools are
highly essential to facilitate the display of useful information
from the wealth of data available in the public repository
Protein Data Bank (PDB) (1). The PDB is an archive of threedimensional biological macromolecular structures determined
experimentally using well-known techniques such as X-ray
crystallography and NMR spectroscopy and is maintained by
the Research Collaboratory for Structural Bioinformatics
(RCSB). The three-dimensional structures are constantly being
used by many researchers all over the world to unravel
the underlying structure–function relationships. Towards this
effort, several crystallographic modeling packages such as
FRODO (2), CHAIN (3), ‘O’ (4) and SETOR (5) are available
to generate and visualize the macromolecules (determined
using the well known physical technique of X-ray crystallography) and its symmetry equivalent molecules. Almost all
these programs have much less control to visualize the symmetry equivalent molecule(s) corresponding to a particular
equivalent position present in the space group. Again, it is
often difficult to save the three-dimensional atomic coordinates
of the user interested symmetry equivalent molecules in the
local machine for further analysis. To the best of our
knowledge, there is no web-based program available
to perform the above operations on all the crystal structures
available in the PDB (1). To overcome this lacuna, with the
least human intervention, the program SEM has been
developed with the following features.
1. Symmetry related molecules around the reference molecule.
2. Molecules within the unit cell.
3. Molecules outside the unit cell.
4. Molecules within and outside the unit cell.
USAGE OF THE SOFTWARE
Towards this end, an efficient methodology has been designed
(Fig. 1) to generate all the molecules within and outside the unit
cell around the reference molecule. In addition, a graphics
display facility has been provided to visualize the molecules and
separate colour schemes have been adopted for the convenience
of the users. The user needs to supply the following information
associated with the given molecule in the appropriate box
provided in the web page: for the three-dimensional crystal
structures, available in the PDB (1), the user needs to provide the
four character PDB-id code. The necessary values (unit cell
constants and space group) will be automatically taken by the
program from the uploaded atomic coordinate file. In addition,
the user needs to choose the space group information from the
pull down menu. The three-dimensional atomic coordinates
of all the structures are available at the locally maintained
anonymous PDB-FTP server, Bioinformatics Centre, Indian
Institute of Science, Bangalore, India. The user needs to provide
the following for the structures uploaded from the client
machine: (i) upload the three-dimensional atomic coordinates in
the PDB (1) format through the web browser; (ii) enter the unit
cell constants (in Å units) and a, b and g (in degrees) in the box
provided; and (iii) choose the space group from the pull down
menu box. The symmetry equivalent points for all the space
groups have been incorporated in the program and the user
needs to choose the correct space group using the pull down
menu to get the corresponding equivalent positions from the
in-built database.
*To whom correspondence should be addressed. Tel: þ91 803601409; Fax: þ91 803600683; Email: [email protected]
Nucleic Acids Research, Vol. 31, No. 13 # Oxford University Press 2003; all rights reserved
Nucleic Acids Research, 2003, Vol. 31, No. 13
3357
Figure 1. Flow chart showing the construction of the symmetry related molecules.
The software is very flexible and has the option of
visualizing all the symmetry equivalent molecules or any
particular molecule generated within the unit cell. In addition,
the user can save the three-dimensional atomic coordinates of
all or any particular molecule(s) in the unit cell into their
local hard disk. To perform this, the user needs to click ‘Click
here to visualize the structures’ and then use the colour scheme
provided in the pop-up window. Using the colour scheme,
the user can choose a particular model or a set of models
whose three-dimensional structure is to be viewed or to be
saved in the local machine.
In addition, the program has an option to highlight a
particular region of the molecule (in different representations)
in the reference and its symmetry equivalent molecules. In this
way, the users can see the role of a particular fragment in the
crystal packing. The public domain graphics program RasMol
(6) has been deployed and incorporated with the proposed
package to visualize the reference and the symmetry related
molecule(s). The user needs to interface the graphics program,
RasMol, with the Netscape browser (only for the first time)
(for instructions: http://144.16.71.11/sem/rasconf.html/). The
program SEM is self-explanatory, easy to use and tested on
Windows 95/98/2000, Windows NT, Linux and SGI platforms
through the most popular WWW (World Wide Web) browser
Netscape. The program is completely general and will work for
most of the space groups available in the International Tables.
The program can be used to see how the molecules are packed
and arranged in the unit cell with respect to the reference
molecule. In addition, this package can be used to generate
the active biological tetramer from the two-homo dimers (7)
like the protein quaternary structure (PQS) file server (8),
Figure 2. This page depicts the typical output of the program SEM for the
PDB-id code: 1UNE (9). Few symmetry equivalent molecules (see checked
boxes in the left panel) (backbone representation with different colours) along
with the reference molecule (white colour ribbon representation) are shown.
Each coloured molecule belongs to a particular symmetry equivalent position
(see left side panel for colouring schemes and other details).
which is an internet resource specially designed to generate the
quaternary assembly. At the general outset, the package SEM
is a very good teaching tool to the students undergoing
graduate programs in structural Bioinformatics and X-ray
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Nucleic Acids Research, 2003, Vol. 31, No. 13
crystallography. The symmetry related molecules of the protein
structure (9) (PDB-id code: 1UNE) generated using this
program is shown in Figure 2.
The program SEM is written using CGI/Perl scripts and can
be executed on our Bioinformatics Linux server [a 3.06 GHz
Pentium IV processor; 1Gb (RD-RAM) of main memory]. The
input data part and the pull down menu of this program are
written in HTML and Java scripts. All the three-dimensional
structures (using the most popular technique, X-ray diffraction)
available in the PDB (1) have been incorporated in this package.
The atomic coordinates are being updated every week and made
available locally in our PDB-FTP server (Bioinformatics
Centre, Indian Institute of Science, Bangalore, India). Hence,
the users can access all the crystal structures available in the
PDB at any given time. In the trial runs, the results appeared in
about 30–40 s depending upon the size of the protein molecule
and the network traffic. Please send your comments
and suggestions for the inclusion of additional options to
Dr K. Sekar ([email protected]).
ACKNOWLEDGEMENTS
The authors gratefully acknowledge the use of the Bioinfomatics
Centre (DIC), the Interactive Graphics Based Molecular
Modeling (IGBMM) and the Supercomputer Education and
Research Centre (SERC). The facilities DIC and IGBMM
are supported by the Department of Biotechnology (DBT),
Government of India.
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