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IARI - RKMP Associated Partners
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Rice Protein Station |
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JMOL: JMOL is a java based viewer for three-dimensional chemical structures.
Several buttons like Select PDB, Schemes, Chain, Molecule colouring, Elements
and amino-acid composition, checkboxes like label, surface (dot surface),
backbone, cartoons, spin were also used for the ease of user.
Select PDB: RPS
contains the list of all known 58 rice protein . User can select its interested
PDB and get its 3D structure in Jmol.
Schemes: RPS contains three schemes:
wireframe, ball and stick, spacefill used to display the structure in Jmol.
CHAIN: User
can get the information about the number of chains in a single protein like
Chain A, Chain B etc.
Color: One can get the information of a molecule on the
basis of its colour; default colour is CPK (colour each atom of the object
according to element,). Colouring of molecules is based on many characteristics
like residues (amino acids), chains, formal charge, Position along chain
(group), molecules, monomers, secondary structure and temperature.
Elements
Present: Composition of a molecule with respect to the elements like carbon,
calcium, nitrogen, hydrogen, phosphorous, sodium etc can be predicted by using
this button.
Amino-Acid Composition: All the protein molecules are made up of
amino acids. Most of the amino acids are common in these protein structures.
However, there are many specific amino acids in each of these proteins.User can
find both of these proteins from this button (amino-acid composition).
Ramachandran plot can also be viewed.
Check-Boxes: Options like label (zoom and label the atoms with their element
atomic symbol and single letter amino acid code, surface (a dotted surface by
using expanded dotted spheres but only surface dots, no dots in the enclosed
volume), backbone (shows the backbone structure of the protein). Also, options
of cartoon and spin are created to show the cartoon structure and spin the
molecule. To use these boxes user have to click on these boxes and also to stop
them.
Refresh: This button is made for the convenience of user, so that he/she
can get back to the basic PDB structure of the desired protein
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This portal belongs to
Indian Agricultural Research Institute, Indian Council of Agricultural Research,
an autonomous organization under the l Research, an autonomous organization
under the r />
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Government of India. Copyright © 2010 IARI
Developed and Maintained by :
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RKMP Team
,, Unit of Simulation and
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