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Visualizing hla-aw with vmd

What follows will be a very brief introduction to what can be done with VMD. Only the most basic viewing functionality will be discussed. For a complete description of the capabilities of VMD and how to use them, please refer to the VMD web site .

In this section, a human leukocyte-associated antigen, HLA-AW (PDB structure ID 2HLA), will be shown under various rendering methods in VMD. This section is intended to convey, first, a general idea of the types of visual representations that are available for protein structures, and second, what information is and is not conveyed by each representation.

VMD allows the user to load and view molecule description files in a wide variety of common formats, including trajectory files with multiple structures of the same molecule, such as might be generated by a simulation. Once the molecules are loaded, the way each molecule is rendered may be controlled using the Graphical Representations menu:

Vmd graphical representations menu

This menu allows the user to control in detail how each molecule is rendered.

Vmd atom coloring methods

Coloring schemes to highlight features of interest.

Vmd molecule drawing methods

Rendering methods in VMD. Which one to use depends on the features to highlight.
The built-in rendering options of VMD.

Molecules may be displayed by various rendering modes:

Hla-aw. drawing method: lines. coloring method: name

In this representation, each line represents a bond between two atoms. The color of each half-bond corresponds to the element of the atom at the corresponding end of the bond (red for oxygen, blue for nitrogen, yellow for sulfur, and teal for carbon). Line representation gives a clear idea of the molecule's connectivity, but for large molecules it can be difficult to isolate protein sub-structures.

Hla-aw. drawing method: vdw. coloring method: name

Here each atom is represented by a sphere whose radius is the Van der Waals radius of the atom. The Van der Waals radius is half the separation of unbonded atoms packed as tightly as possible, and provides a rough notion of a collision radius, although it is not a firm barrier. This representation of the molecule gives a rough sense of its shape, and is sometimes called a space-filling model.

Hla-aw. drawing method: vdw. coloring method: chain

This rendering is the same as in the previous figure, except that now the atoms are colored based on which polypeptide chain they belong to. HLA-AW consists of two chains, the alpha chain (blue), which folds into three domains and the smaller β2 microglobulin (red), which is a component of a whole class of HLA proteins. Coloring by chain allows an inspection of how the polypeptide subunits come together to form the whole quaternary structure of the protein. The black balls are water molecules near the surface of the protein that always appear in the same place in crystal structures, and may therefore be considered part of the structure for some applications.

Hla-aw. drawing method: surf. coloring method: chain

The Surf drawing mode renders a surface swept out by a sphere of some set size skimming the protein. Usually, this size is approximately that of a water molecule, in which case the rendered surface is very similar to the solvent-accessible surface . Note that it is impossible to deduce the connectivity of the atoms from this image or from the space filling image in the previous figure. Overall shape, rather than connectivity, is the information conveyed by these representations. Hence, both backbone-based and surface-based renderings are necessary to fully understand a protein's structure.

Hla-aw. drawing method: surf. coloring method: chain

Here the protein has been rotated approximately 90 degrees toward the viewer, so that, compared to the previous image, we are looking down from above. The deep groove running from the top left to lower right is the binding pocket of the protein.

Hla-aw. drawing method: cartoon. coloring method: chain

Cartoon rendering places an emphasis on secondary structure. Beta sheets appear as flattened arrows, and alpha helices appear as cylinders. These are common conventions in representing protein secondary structure. By examining this image, we can see that the walls of the binding pocket observed in the previous figure consist of alpha helices, and the floor is an anti-parallel beta sheet. In anti-parallel beta sheets, adjacent strands run in the opposite direction (notice the arrow points alternate in direction). Note that this representation only conveys information about the backbone connectivity of the protein. Side chain atoms are omitted, and therefore the overall shape is only a very coarse approximation.

Hla-aw. drawing method: surf. coloring method: restype

Alternative coloring methods can provide additional insight into a protein's structure and function. Here each atom is colored based on whether the side chain of the amino acid residue to which it belongs is acidic (red), basic (blue), polar neutral (green), or apolar (gray). Note that residues on the surface of the protein tend to be hydrophilic (attracted to water, in red, blue, and green), whereas residues closer to the core of the protein tend to be hydrophobic (greasy or water repellant, in gray). This is characteristic of proteins that exist in aqueous solution in nature. Their native structure is stabilized by a tendency for the hydrophilic residues to interact with the solvent water molecules, while the hydrophobic residues are driven together away from the solvent. Clusters of hydrophobic residues on the surface often indicate a location that is usually protected from solvent in the natural state, either by interaction with another molecule or by part of the protein itself.

Questions & Answers

where we get a research paper on Nano chemistry....?
Maira Reply
what are the products of Nano chemistry?
Maira Reply
There are lots of products of nano chemistry... Like nano coatings.....carbon fiber.. And lots of others..
learn
Even nanotechnology is pretty much all about chemistry... Its the chemistry on quantum or atomic level
learn
Google
da
no nanotechnology is also a part of physics and maths it requires angle formulas and some pressure regarding concepts
Bhagvanji
Preparation and Applications of Nanomaterial for Drug Delivery
Hafiz Reply
revolt
da
Application of nanotechnology in medicine
what is variations in raman spectra for nanomaterials
Jyoti Reply
I only see partial conversation and what's the question here!
Crow Reply
what about nanotechnology for water purification
RAW Reply
please someone correct me if I'm wrong but I think one can use nanoparticles, specially silver nanoparticles for water treatment.
Damian
yes that's correct
Professor
I think
Professor
Nasa has use it in the 60's, copper as water purification in the moon travel.
Alexandre
nanocopper obvius
Alexandre
what is the stm
Brian Reply
is there industrial application of fullrenes. What is the method to prepare fullrene on large scale.?
Rafiq
industrial application...? mmm I think on the medical side as drug carrier, but you should go deeper on your research, I may be wrong
Damian
How we are making nano material?
LITNING Reply
what is a peer
LITNING Reply
What is meant by 'nano scale'?
LITNING Reply
What is STMs full form?
LITNING
scanning tunneling microscope
Sahil
how nano science is used for hydrophobicity
Santosh
Do u think that Graphene and Fullrene fiber can be used to make Air Plane body structure the lightest and strongest. Rafiq
Rafiq
what is differents between GO and RGO?
Mahi
what is simplest way to understand the applications of nano robots used to detect the cancer affected cell of human body.? How this robot is carried to required site of body cell.? what will be the carrier material and how can be detected that correct delivery of drug is done Rafiq
Rafiq
if virus is killing to make ARTIFICIAL DNA OF GRAPHENE FOR KILLED THE VIRUS .THIS IS OUR ASSUMPTION
Anam
analytical skills graphene is prepared to kill any type viruses .
Anam
Any one who tell me about Preparation and application of Nanomaterial for drug Delivery
Hafiz
what is Nano technology ?
Bob Reply
write examples of Nano molecule?
Bob
The nanotechnology is as new science, to scale nanometric
brayan
nanotechnology is the study, desing, synthesis, manipulation and application of materials and functional systems through control of matter at nanoscale
Damian
Is there any normative that regulates the use of silver nanoparticles?
Damian Reply
what king of growth are you checking .?
Renato
What fields keep nano created devices from performing or assimulating ? Magnetic fields ? Are do they assimilate ?
Stoney Reply
why we need to study biomolecules, molecular biology in nanotechnology?
Adin Reply
?
Kyle
yes I'm doing my masters in nanotechnology, we are being studying all these domains as well..
Adin
why?
Adin
what school?
Kyle
biomolecules are e building blocks of every organics and inorganic materials.
Joe
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Source:  OpenStax, Geometric methods in structural computational biology. OpenStax CNX. Jun 11, 2007 Download for free at http://cnx.org/content/col10344/1.6
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