WebLabViewrLite Tutorial www.msi.com

Jean-Yves Sgro

Informations

• Publié par: Phoon
• Nombre de lectures: 40
• Langue: English

Extrait

WebLab Viewer Exercise C: Publication Quality Structures with
WebLabViewerLite
WebLabViewerLite is a free software from MSI,Inc. (http://www.msi.com) that runs equally well
on Macintosh or Wintel computers. The program can be downloaded from
http://www.msi.com/weblab/viewer/download.html
This software is in part based on Rasmol but it’s interface is very different. However it has
incorporated within it the Silicon Graphics 3D rendering language which makes it a very powerful
visualization software and can help create publication-quality images on a desktop computer. A
“Pro” version of the software is also available, it allows the modeling of side chains and other
complex calculations.
We will use only the Free Lite version in these exercises.
For a quick overview of a protein the use of Rasmol or Chime might be more time efficient.
WebLabViewer is completely mouse-driven with many menu options and choices. In addition
WebLabViewer will let you save the file in the “visual state” that it is in, color choices, types of
representations, lablels etc., therefore allowing you to save time the next time you want to explore
that particular file.
1) Open the WebLabViewer program
2) Open the PDB file3cro.pdb with the File/Open... menu
Typically the program will show the structure in stick model with CPK colors when it opens
a standard PDB file. Within the graphics window you can rotate the structure as symbolized
by the circular rotating arrow in the second position within the floating window at the left.
The other selections would be used for translation, close or far movement, or for
manipulating side chains with torsion angles. The first button is an arrow and can be used by
clicking to select an atom or by dragging to select a group of atoms.
3) Select the menu View/Display Style...
A box will open with 4 buttons at the top: Atom | Protein | Cell | RNA/DNA

Click one of these buttons, you will be presented with a series of options:
Atom Protein Cell RNA/DNA
Off Off Off Off
Line CA Wire Line Ladders
Ball and Stick CA stick Stick Rings
CPK Line ribbon Arrows
Polyhedron Flat ribbon
Solid ribbon
Tube
Schematic
The option Cell referers to the crystallographically relevant cell dimensions related to the crystal
structure and will not be useful for our purpose.
(Note: if you do now see all these options you may need to go into theEdit menu and choose
Select All...)
M02 - 64-4) Selecting a display style for each molecule:
We will now modify the options for each of these to obtain a nice display:
Click on the Atom button, and select OFFProteinSchematicRNA/DNAArrows
Click the OK button and you should see an image where the protein is presented as a series of
cylinders representing the alpha helices and the DNA with each strand represented as an arrow.
You can use the mouse to rotate the image within the graphics window.
You can test a few more combinations on your own, for example make the protein a Solid ribbon
and the DNA a Ladder. We will see later on the best usage of the Atom selections.
5) Modifying colors:
For each style of representation of a given type of molecule there is a choice of prearranged colors
which are useful and listed in the following table.
Atom Protein Cell RNA/DNA
Element Residue Residue
Parent Color Hydrophobicity Base Tpe
Charge pKa Nucleic Acid Chain
Nucleic Acid Secondary Type Molecule
Nucleic Acid Chain Amino Acid Chain Cell
Molecule Molecule
Cell Cell
Amino Acid
Amino Acid Chain
Chain
Select again the menu View/Display Style... In the menu bar
Click on Protein
for Style select Solid Ribbon
for Color By.. Select Amino Acid Chain
Click on RNA/DNA
for Style select Ladders
for Color By.. Select Base Type
Click the OK button
These preset colors are very useful but as an alternative the button Custom will open a color wheel
for choosing a color you choose.
M02 - 65-6) Selecting atoms and residues with the mouse:
The selection of atoms, residues, bases or objects can be accomplished either with a mous, from a
hierarchy listing of all atoms within a separate window or from a select menu. Let’s first test our
ability to select with the mouse.
Your mouse cursor should for now be the rotating arrow. In normal mode you simply click within
the graphics window and moving the mouse will rotate the display. However if you click on a DNA
ladder currently displayed but do not start a rotation that ladder will be colored yellow, which means
it is selected. Similarly you could select one residue within one of the alpha helices of the displayed
proteins.
To graphically select larger segments of a molecule within the display you would need to switch to
the selection arrow at the top of the small floating window. With this cursor selected you can now
click and drag within the graphics window, the structures will not rotate but areas will be selected
colored yellow as a visual cue of their selection.
Once a residue or an area is selected, the commands that will be executed next will be applied only
to the selected group of atoms colored yellow.
Select the arrow cursor at the top of the floating window (simple arrow)
Click on one of the bars on the DNA ladder
While pressing the Shift key click on another bar to collectively select those bases
The selected bases are now colored yellow to indicate that they have been selected. We can now
decide to apply various graphics options to them. For example we are now going to make them
stand out as space filling representations:
Select the menu View/Display Style...
In the Atom option box select CPK for Style
Click the OK button
7) Selecting atoms and residues with the Hierarchy Window:
Selecting with the mouse can be best in some cases, but if the graphic
display is busy with many molecules or if the molecule is large it may be
difficult to locate the correct atoms or group of atoms to choose. In these
cases the use the the Hierarchy Window is the best option.
In the Window menu select the Hierarchy View option. This will open
a new window, which can be resized if it too large. The best shape for this
window is to make it long and narrow. When the window is first opened it
shows a list of a single item: Cell. This represents the crytallographic
region of space which contains the structure. Clicking on the triangle on
the side will show the logical content of the Cell. In this case the name of
the PDB file. Clicking on this triangle will list the logical content of the
PDB file as the names of the DNA strands (A and B) and the name of the
protein chains (L and R) as well as the waters. The hierarchichal display
continues as the list of amino acids or nucleotides, which themselves
contain the final list of the atoms and the bonds between them:

Do the following actions:
Open Window/Hierarchy Window
Click on the A chain
Hold the SHIFT key and click on the B chain (Both A and B should be yellow)
Select the menu View/Display Style...
In the Atom option box select Ball and Stick for Style
Click the OK button
M02 - 66-Note: The ball-and-stick option was applied only to the selected items. This is a general rule, where
modifications will be applied only to the current selection. In this fashion, complex combinations of
graphics types can be achieved, applied to specific portions of any molecule within the display.
8) Selecting specific atoms with the select menu:
The selection of a specific atom, group of atoms or residues is very important in the creation of an
image. There is yet a third technique to select items within this software located in the Edit menu
with the following options:
Select All
Select parent
Select....
Invert selection
The Select... Option brings a dialog box with further refinement of the selection query. By default
the 2 otions Type and Element are checked at opening. The options available in these 2 sets are
listed in the table at right:
Type Element
Cell O
Molecule C
Nucleic Acid Chain N
Nucleic Acid P
Atom S
Bond
Amino Acid Chain
Amino Acid
Chain
The dialog box offers 4 buttons to select or deselect the selection listed in the left part of the box.
For example the image above shows the box with Type as Atom and Element as Oxygen. With
this selection in place pressing the Select button at right would select all the oxygen atoms within
the model displayed. Pressing the Deselect button would remove all oxygen from the previously
selection group of atoms.
Note that many options within the type item will gray-out the Element option.
Exercise: make all the Phosphorus atoms orange.
Select the Edit/Select.... menu item
Within the dialog box select Atom in the Type option and P in the Element option
Click on the Select button at right. The phosphorus atoms will appear yellow within the
graphics display.
Select the menu View/Display Style...
In the Atom option box select CPK for Style, select the Custom Color button and click
within the color square next to it. A color wheel will appear, select an orange color
Click the OK button
You should now see large atoms in the display within the DNA strands colored with the
selected orange color.
M02 - 67-Exercise: select all the C & G within the DNA and color them white in CPK style
Select the Edit/Select.... menu