WebLabViewrLite Tutorial www.msi.com

WebLabViewrLite Tutorial www.msi.com

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WebLab Viewer Exercise C: Publication Quality Structures withWebLabViewerLiteWebLabViewerLite is a free software from MSI,Inc. (http://www.msi.com) that runs equally wellon Macintosh or Wintel computers. The program can be downloaded fromhttp://www.msi.com/weblab/viewer/download.htmlThis software is in part based on Rasmol but it’s interface is very different. However it hasincorporated within it the Silicon Graphics 3D rendering language which makes it a very powerfulvisualization 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 othercomplex 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 additionWebLabViewer will let you save the file in the “visual state” that it is in, color choices, types ofrepresentations, lablels etc., therefore allowing you to save time the next time you want to explorethat particular file.1) Open the WebLabViewer program2) Open the PDB file3cro.pdb with the File/Open... menuTypically the program will show the structure in stick model with CPK colors when it opensa standard PDB file. Within the graphics window you can rotate the structure as symbolizedby the circular rotating arrow in the second position within the ...

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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 item
Within the dialog box select Nucleic Acid in the Type option
(The Element option will become dimmed)
In the Name box write the letter C
Click on the Select button at right.
The atoms composing the C nucleotides will
appear yellow within the graphics display.
In the Name box write the letter GC
(Note that cliking on “select” has an additive
effect and now both C and Gs are selected
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 the white color at the center of the wheel.
Click the OK button.
In the same manner complex selections can be achieved by selecting either the select or the
deselect buttons located on the right hand side of the Select dialog box.
Hint: often to know where specific amino acids, side chains, or nucleic acid fragments the easiest is
to select them, color them a bright color such as red, yellow or white and give it a CPK space filling
size.
9) Molecular surface:
WebLabViewerLite can create beautifully rendered molecular surfaces of whole or portions of
molecules. The surface can be colored as a single hue, an electrostatic potential and can be made
transparent.
A histine amino acid is represented in stick model with
the van der Waals radii of the atoms shown as lined
spheres. A probe of radius R=1.4Å (the size of a water
molecule) can be rolled over the atoms. A surface can
be constructed by connecting all the points following
the center of the probe (Accessible), this is usually
refered ton as “solvent accessible surface”. By its
definition this surface is always convex. Its volume
appears larger than the space occupied by the vn der
Waals enveloppes. Alternatively the surface can be
defined as the series of points where the probe touches
the van der Waals sphere (Contact + Reentrant). In this
case the contact areas are convex while the reentrant
surface areas are concave. This surface is usually
refered to as “molecular surface” and follows the van
der Waals radii more closely, as Saran Wrap around
peas in a dish placed in the microwave...
WebLabViewer Lite defines the following options for
Ref.: Richards F.M., Areas, volumes, packing andnaming surfaces which are unfortunately not the usual
protein structure. Ann. Rev. Biophys. Bioeng. 1977,standard and can be confusing in their name:
6:151-176(WebLab) (Common Litterature)
Soft = solvent accessible
Solvent = molecular surface
M02 - 68-Exercise: creating a quality image with mixed rendering including surface
Close all windows from previous exercises. If necessary quit and restart the program.
Open the 3cro.pdb file
Orient the file so you can easily recognize the proteins from the DNA molecule
In the menu Window/Hierarchy View select the proteins, which are chains L and R
(drag the mouse to select both or click on L and holding down the SHIFT key click on R)
Once the proteins are selected they become yellow.
Select the menu View/Display Style...
In the Atom option box select Off for Style
Click on the Protein tab, and select the schematic option in the pulldown list
Click the OK button
While the proteins are still selected, although now not visible on the screen, select the
Tools/Surfaces>add menu option. This will automatically calculate a surface around the
protein atoms. (there may be a delay due to the complexity of the calculation).
To alter the surface appearance it first needs to be selected.The easiest way is to click on the
words “Solid Surface” which has now appeared within the Hierarchy View window.
Select the menu View/Display Style...
Style Color By
OFF Parent Color
Solvent Electrostatic Potential
Soft Atom Charge
Van der Waals Atom color
The default is called a Soft surface representation. Switch to the Solvent surface option. The Probe
Radius should be 1.4Å (the average sphere size occupied by a water molecule).
You will observe that the solvent surface is smaller than the soft surface (see inset above)
In the Color By select the Electrostatic Potential option.
Click OK
The surface will be altered to the specified option.
M02 - 69-
Select the Water molecules from the Hierarchy View window.
Select the menu View/Display Style...
Under the Atom tab select Off.
Select the DNA strand A
In the Style option select Rings
Use the custom color option and make it orange/yellow or a color you like.
Click OK
Select the DNA strand B
Select the menu View/Display Style...
In the Style option select Rings
Use the custom color option and make it light-blue/cyan or a color you like.
Click OK
Select the DNA strands A and B
Select the menu View/Display Style...
The Style option should show Rings
In the coloring part of the window select the option Residue
Click OK
The DNA should now appear as colored by base (A,C,G,T) of different colors, and
the backbones of strands A and B should be of different color. The surface should
appear as a molecular surface colored by electrostatics. You can observe and orient
the DNA/protein complex to see the best interdigitaion of the protein within the
DNA and also observe the location of the blue (positive) charges in relation to the
DNA backbone.
The background is currently black.
The Edit/Preferences menu provides 5 tab sections: Display, Import, Lighting,Tools, View
Click on the Lighting tabBackground Color rectangle, currently black, and a colorwheel window will
appear.
M02 - 70-
The color selection can function in various modes, the easiest is the Hue/Saturation/Value (HSL)
mode, which should be the default. HSL can be selected from the button list on the left hand side of
the panel. While in this mode within this window, glide the cursor from 0 to 100% at the bottom of
the window. The circular wheel should go from total darkness to an array of colors. The selector
cursor is by default located at the center of the wheel, and when the value of the bottom cursor is
changed from 0 to 100 the color varies from black, to white in the center of the wheel. That is the
option we want as white is a good background color for final printing, but at least is easier on the
printer cartridges. Click OK you are now returned to the preferences panel.
Back at the preferences panel click on the Display tab. This
is where you can select to add Depth Cueing to your
representation. This is also sometimes called “fogging in”
and it’s purpose it to add three dimensionality and ddepth to
your rendering. It is not always best to engage this option,
you can try it to see how your perception may be changed.
For the final image rendering you would want to engage the
High option within the Quality section of this panel.
10) Saving the final image:
Make sure you have oriented the molecules in order to show the mutations or other features at their
best. You should have selected the High option in the Quality panel within the Display tab of the
File/Preferences menu.
Once everything is as you want, go in the File/Save As.... menu.
A dialog box will open, at the bottom of which a pull-down menu will let you select the format you
want to save your representation.
To save an image, select the Picture File option.
Change the name of the file to be saved accordingly. On a Macintosh, the file will be saved in
Macintosh PICT format. (On a windows system the image file format would be GIF).
The next window will ask the image size that you desire, proposing the current window size as the
default. You want to enter here the largest numbers that your computer memory will allow, as larger
files provide smoother final prints. Example of full screen sizes could reflect the sizes available for
multiscan monitors (Height x Width): 640x480, 800x600, 1024x768, 1024x1280,1200x1600. At
the latter resolution , this image is less than 1Mb on a Macintosh (860Kb). All images are saved at
the standard screen resolution of 72 dpi (dots per inch).The resolution can be adjusted at a later
stage within Photoshop or equivallent program.
Resolution: common misconceptions.
The word resolution is often used inappropriately which can result in a lot of confusion. The following discussion
only applies to “raster” images (the kind we are making here, as opposed to “vector-based” images).
A computer raster image is a clearly defined entity: it is composed of a series of single pixels (dots) in rows (lines).
M02 - 71-The number of pixels is defined along the length and the height, just like a rectangular piece of land. For example we
can have an image with 648 pixels along its width and 504 pixels in height, the image is therefore 648 x 504
pixels. It is not a resolution, but an absolute “measure” of the file.
Resolution is often cited as dpi or dots-per-i nch, where a “dot” represents a pixel. This simply states how many
pixels will be used to make up one inch of the final print. Common measures of resolution are 72 and 300 dpi. If
the file is printed at 72 dpi, each inch will use up 72 pixels,
72 dpi:
300 dpi
Therefore the example image would have the following physical print size: 648 / 72= 9 inches wide and 504 / 72 =
7inches high. If on the other hand the printing resolution is 300 dpi, 300 pixels will be used for each inch of the
print, and therefore the final physical print size will be smaller: 648 / 300 = 2.16 inches wide and 504 / 300 = 1.68
inches high.
Conclusion: The images created have a finite, well defined number of pixels. The final physical size of the image is
determined by how many pixels are used up to make one inch of the final print. The more pixels are used, the
smaller the image. On the other hand, placing more pixels in a smaller area makes the image more smooth and less
“blocky”. It is said to have a better “resolution”.
How to choose the printing resolution of your image: Open the image in PhotoShop, select the Image/Image
Size...menu. Unselect the “Resample Image” button, and only then change the “Resolution” value from 72 to 300.
10) Self paced testing exercise: (jump directly to the next section if you are short on time.)
Using the knowledge you just acquired, make a depth cued molecular surface image of myoglobin
with the file myoglobin.pdb , and show the iron (Fe) and Oxygen (O1 and O2) atoms in CPK
space filling.
You can use color to help distinguish the various elements. You can use the hierarchy window to
guide you in the selection of the Heme. You can explore the effect of light direction from the
Edit/Preferences/Lighting tab. You can also use the file 1ccr.pdb of Cytochrome C which has
also a heme structure.

M02 - 72-