WebLab Viewer 3D

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????WebLab Viewer??3D????

• Ta-Wei Li
• NCTU

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Start to use WebLab Viewer Pro

• Click two times on WebLab Viewer Pro ??
• Go to View Tool Bar and select all the tools,
  such as

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Draw Chain Molecules

• All atoms drawn directly by sketch pen are
  carbons unless you specify otherwise.
• Select sketch pen
• Click an empty area to draw the first C atom
• Move the cursor to another empty are to draw the
  2nd, 3rd and 4th C atom

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Add H atoms to C backbone

• Click select button
• Select the whole molecule. There are two ways
• Circle all four C atoms
• Click any one C atom. Then, with pushing
  ltShiftgt, click other three C atoms.
• Click Add Hydrogens button

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Eye-check and Clean Structure

• Click Zoom button and drag the mouse to
  zoom and investigate butane structure
• Click Translate button and drag the mouse
  to rotate and check butane structure
• Click Rotation button and drag the mouse
  to rotate and investigate butane structure
• Now, click Clean button and recheck the
  butane molecule again

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Hand-check Structure 1

• Bond Length
• Select any two neighboring C atoms and Click
  Tools Monitors Distance
• Distance
• Select the two farthest H atoms and Click Tools
  Monitors Distance
• Bond Angle
• Select any three neighboring C atoms and Click
  Tools Monitors Angle
• Then click Tools Monitors Remove

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Hand-check Structure 2

• Torsional Angle
• Select four neighboring C atoms and Click Tools
  Monitors Torsion

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What is Clean Structure ?

• It is to search local energy minimum point.

Energy
C
A
B
Molecular Geometry
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Energy Profile of n-Butane

• Local
• Minima

Global Minimum
?
?
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Find other Local Minimum

• Click Torsion button
• Then click the middle C-C bond and drag the mouse
  to change the torsional angle into 90
• Now, reselect the whole molecule and click
  clean button to see if you get the gauche
  structure, whose trosional angle is close to 60.

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Change Atomic Type

• Select the first C atom and click modify
  Element O
• Select the forth C atom and click the right
  button of the mouse, Change Element O
• Click clean to get one local minimum of 1,2
  ethanediol (???)

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Copy, Paste and Move

• Select whole 1,2 ethanediol.
• Click edit copy
• Click edit paste
• Drag the new 1,2 ethanediol to empty area
• You may change any torsional angle and click
  Clean button to get another local minimum of
  1,2 ethanediol.

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WebLab Practice and Discussion 1

• How many local minimum of 1,2 ethanediol may
  contain intramolecular H bond (?????), I.e., the
  distance between O and H is ranged from 1.5 to
  2.5 Å?
• In the same file, please draw the following
  structures and show bond angles of CH4, BH3, NH3,
  H2O.

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Draw BF3 (1)

• Open WebLab with Clicking
• Select sketch pen
• Click an empty area to draw a C atom
• Change C into B
• Click Add Hydrogens button
• Change H into F and then click clean
• Whats wrong?

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Draw BF3 (2)

• The hybridization of BF3 is sp2, but not sp3.
• The structure of BF3 should be a plane , and ?FBF
  should be 120.
• Please check if ?FBF is 120.
• In fact, current structure of BF3 looks like NH3.
• Select B, and then click Modify
  Hybridization sp2.
• Click Clean to see if you get the correct
  structure of BF3 .

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Draw CH2BrCl

• Select sketch pen and click another empty area
  to draw C atom
• Click Add Hydrogens button
• Change one H into Br and another into Cl
• Now, select this molecule CH2 BrCl.
• Copy, paste and move CH2 BrCl, like

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Make Mirror Image

• Now, rotate the second CH2BrCl to be the mirror
  image of the first one ,such as
• Now, we can say these two molecules are identical.

Mirror Image
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Create Stereoisomers

• For both CH2BrCl, change one H into I, such
  as
• Are their structures still the same?

Mirror Image
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Understand Chiral Center

• No, they are not the same configuration.
• A carbon atomto which four different group are
  attached is a chiral center.

Configuration R
Configuration S
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Check the Chirality

• Select both CHIBrCl
• Click View Display Style
• In Atom Display Style, select Line
• Click Tools Monitors Chirality

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Draw cyclodecane, cyclohexane and cyclopentane
(1)

• Select ring pen
• Click an empty area and drag the mouse to draw 10
  C ring
• Click Add Hydrogens and Clean
• Click an empty area and drag the mouse to draw 6
  C ring
• Click Add Hydrogens and Clean
• Click an empty area and drag the mouse to draw 5
  C ring
• Click Add Hydrogens and Clean

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Draw cyclodecane, cyclohexane and cyclopentane
(2)

• Do you know which cyclic aliphatic compound is
  more relaxed than others?
• Please check ?CCC of cyclodecane, cyclohexane
  and cyclopentane?

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Understand Cyclohexane

• Consider that 6 C atoms lie in a plane
• The bonds in the plane are called equatroial
  bonds.
• The bonds above and below the plane are called
  axial bonds

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Understand 1,3-diaxial interaction

• Please draw equatorial-methylcyclohexane and
  axial-methylcyclohexane.
• Are the the same compounds?
• Which is the more crowded compound?

?
?
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Draw Benzene

• Select ring pen
• Click an empty area and drag the mouse to draw 6
  member ring
• Select the whole molecule and click Aromatic
  bond button
• Click Add Hydrogens and Clean

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Hole Checking

• Please select cyclopentane, cyclohexane,
  cyclodecane and benzene.
• Click View Display Style
• In Atom Display Style, select CPK
• Check if there are holes in the middle of those
  molecules.
• If you want to change the background color, click
  View Option Background and select
  distinguishable color.

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Draw Decalin

• Select ring pen
• Click an empty area and drag the mouse to draw 6
  C ring
• Click one bond of the 6 C ring
• Click Add Hydrogens and Clean to get decalin
• Are H on the bridge C of decalin equatorial or
  axial H?

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Draw H bond of Water

• Select sketch pen
• Draw two separate C atoms and change them into
  O
• Click Add Hydrogens and Clean
• Select and move H atom towards O of another water
  molecule
• After clicking clean, measure distance of H
  bond for water.

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WebLab Practice and Discussion 2

• For equatorial-methylcyclohexane and
  axial-methylcyclohexane, which is the more
  crowded compound? why?
• Among cyclic aliphatic compounds, which has a
  hole in the middle, and which is more relaxed?
  Please explain why it is more relaxed.
• Are H on the bridge C of decalin equatorial or
  axial H?
• What is the distance of H-bond for water?

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What is protein?

• Protein is polymer of Amino Acids.

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Study a protein molecule Trypsin

• Select the Open command on the File menu and
  select the Trypsin.msv file in the QuickStart
  folder.
• Select View/Display Style to open the Display
  Style dialog box. Move the panel off to the side
  where it does not block your view of the trypsin
  model.
• In the Display Style dialog box, click on the
  Protein tab to go to the Protein page (which
  wasn't visible in our previous exercises with
  luciferin). Under Display Style, try various
  combinations of Display Style and Coloring
  combinations.

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Protein-specific displays

• Select Atom. Turn Off the Atom Display Style and
  click OK
• Select Protein. On the Display Style, select Flat
  Ribbon and
• Color By Residue click Apply.
• Color by Hydrophobicity and click Apply.
• Color by Secondary Type and click Apply.

• On the Display Style, select Schematic and
• Color By Secondary Type click Apply.
• On the Display Style, select Ca Stick and
• Color By Residue Type click OK.

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Structure of Protein (1)

• Primary Structure Amino acid sequence
• Secondary Structure Arrangement of chain about
  an axis
• Alpha Helix
• Beta Sheet
• Tertiary Structure Spatial relationship of
  amino acid units that are relative far apart in
  the protein chain

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Structure of Protein (2)
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S-S intramolecular linkage

• In the Display Style dialog box, apply the Line
  Display Style to the Atoms and then Color by
  Element. Click OK. From the Edit menu, open the
  Select dialog box by clicking Select.... Toggle
  on the Element parameter and type S in its text
  box. Click Select.
• Open the Display Style dialog box and go to the
  Atom page. Select stick in the Atom Display Style
  and click OK

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Investigating H-bonding

• Select the Tools / Monitors / Hbond command. Then
  click in an empty part of the document to
  unselect the hydrogen bond monitor.
• Open the Display Style dialog box. Go to the
  Protein page and turn on Solid Ribbon Display
  Style. Don't change the coloring. Click Apply.

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Four Ways to Link Protein
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Projecting properties onto surfaces

• Select the Tools / Surfaces / Add command.
• Open the Display Style dialog box and click on
  the Surface tab. Turn on the Transparent option
  and click Apply.
• When you are done experimenting with the
  surfaces, close the trypsin document. Use Save
  as... and rename your file if you want to save
  your view, or select File / Close and reply No to
  the prompt if you do not want to save your
  version.

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What does surface mean?
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What is DNA ?

• DNA is polymer of nucleotide.

BASE A, T, G, C
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Customized display features for DNA Yeast DNA
and protein

• Use File / Open or one of the other open methods
  to load the Complex.msv file.
• Open the Display Style dialog box and click on
  the DNA/RNA tab. Set the Display Style to Ladder
  and the coloring to Color by Residue. Click
  Apply.
• Click the Protein tab and set the Display Style
  to Tube. Set the coloring to Secondary Type.
• Go to the Atom page and turn Off the Atom Display
  Style. Click OK to close the dialog box.

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Hierarchy window (1)

• Go to the Window menu and select New Hierarchy
  Window. After the window opens, select Window /
  Tile Vertical. (If you have additional Weblab
  Viewer documents open, close them or minimize any
  that we are not using and then resize the 3D and
  Hierarchy windows for this lesson to fit side by
  side.)

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Hierarchy window (2)

• Be sure the 3D window is active, then use the
  Display Style dialog box to set the Atom Display
  Style to Ball and Stick Color by Residue.
• In the Hierarchy window, click with the Selection
  tool on the box for C3'1 to expand the
  hierarchy to show the atoms within this amino
  acid chain. Click on the small structure icon
  next to C3'1 to select it and see the information
  reported in the Task bar pane Nucleic Acid
  C3'1.
• With C3'1 still selected, select Edit /
  Properties to get more information about this
  object.

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Hierarchy window (3)

• Click on the Visibility tool to change to
  the Visibility mode and click on the small
  structure icon next to C3'1.
• Click on various amino acids within the C3'1
  amino acid. Then click on the O5 atom and
  ltShiftgt- click on the C6 atom. Try various
  combinations of selecting an object or a range of
  objects.
• Finally, click with the Visibility pointer in an
  empty area of the Hierarchy window.

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Hierarchy window (4)

• Click the - box for the first residue, C3'1.
  Click the small structure icon with the
  Visibility tool and then ltShiftgt-click each
  object in turn down until all the residues in
  Chain D are displayed. ltShiftgt-click on the
  chain-link icon for Chain D to add the backbone
  to the display.

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Crystal properties Pyrite

• Open the pyrite.msv file in the QuickStart
  folder. To simplify window management, close any
  documents from the earlier lessons.
• First, use the Rotate tool to simply rotate and
  observe the model. Hold down the ltShiftgt key and
  drag the mouse around the window to rotate about
  the Z axis.

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Using crystal display options (1)

• Open the Display Style dialog box and click the
  Cell tab. The Lattice Display is already set to
  Line. Click in the color box to open the Color
  Picker and pick a lighter gray. Click OK.
• Turn on the Label Axes option and click Apply in
  the Cell page of the Display Style dialog box.
• On the Atom page, change the Display Style to
  Ball and Stick. Change the Stick size to 0.1.
  Rotate the model again.

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Space Group

• Open the Crystal Builder dialog box by selecting
  the Tools / Crystal Cell... command.
• Click the Space Groups tab of the Crystal Builder
  dialog box to see the symmetry group

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View More Cells

• Click the Preferences tab.
• On the Preferences page of the Crystal Builder
  dialog box, set the View Range for the A, B, and
  C axes each to 2. Click Apply. (You may want to
  close the Crystal Builder panel and use the Fit
  to Screen tool so you can see the entire lattice,
  then open the Crystal Builder panel again.) Then,
  on the Preferences page, set the Symmetry Style
  option to Positions and click Apply.

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WebLab Practice and Discussion 3

• How many alpha helixes and S-S linkages in
  Trypsin?
• How many polypeptide chains and DNA chains in
  Yeast DNA complex?
• In Yeast DNA, are the number of C-G pairs more
  than A-T pairs?
• What is the formula of pyrite? Which atom is on
  the face-centered position? How many atoms are
  next to the face-centered atom?