Short Manual for Quick Reference

Manual

Content

Tool Icons

1. Rendering attributes for main window.
2. Translate (Holding F5, F6 or F7 translate only on x, y, z axis)
3. Zoom (move the mouse left and right)
4. Rotate (Holding F5, F6 or F7 rotate only around x, y, z axis)

(Use "Tab" to change the currently active tool between B, C, D)

5. Measure distance between two atoms. (Pick two atoms)
6. Measure angle between three atoms. (Pick three atoms in sequence)
7. Measure w , f and y angles of the picked amino acid (pick any atom of the AA). But when this tool is invoked with the Ctrl key, it will ask you to pick four atoms to measure the torsion angle of any specific bond.
8. Label the picked atom. ( Alt-[minus] clears labels )
9. Display groups within a certain distance from an atom.
10. Center the molecule on one atom.
11. Fit a molecule onto another.
12. Mutate a residue. Click on this icon, select one atom in the group and pick the replacement from pop-up menu, then click this icon again.
13. Rotate around bonds. Click on this icon, select one atom in the group. Make changes and click this icon again.

(a) Holding down key "1" while moving clicked mouse rotates the CA-CB bond; key "2" for CB-CG bond etc.
(b) Holding down key "9" or "0" will alter the f and y angles respectively.

(Alternatively, after you pick the side chain, you could click the little arrows appearing at the right of the torsion tool icon to modify the torsion angles. The little arrows appearing at the bottom of the torsion tool icon would affect the f and y angles.)

When "Caps Lock" is down, you are in the "repeated" mode. That means you could do the measurement, labeling successively. If you want to escape the "repeated" mode, just hit "Esc" button.

Control Panel:

The Header

• The name of the current molecule or "layer": when multiple molecules are loaded, clicking here brings up a selection list.
• Checkboxes: Visible: when this box is checked, the molecule in the current layer is visible. Movable: when this box is checked, this molecule is movable.

The Control Panel List

• "Group" column: Name of each individual building block of the model called a "group". (I.e. each amino acid, water, nucleic acid.)
• Chain and secondary structure information will also be shown in the left of group name.
• "Show" column: If checked, the corresponding group is visible.
• "Sidechain" column: If checked, the group’s sidechain is visible.
• "Label" column: If checked, label the group. (label format could be selected from "Label Kind" of "Display" menu )
• "van der Waals dots spheres" column: If checked, show a dotted surface for that group.
• "Ribbon" column: If checked, a ribbon is drawn over that group.
• "Color" column: Click to select the group’s show color.

Some manipulating tricks:

1. Like Windows’ manipulation, holding "Control" key allows a discontinuous selection, while holding the "Shift" key for continuous selection. (For "group" column only)
2. Clicking right mouse button on a group name centers its a carbon in the view.
3. Except for "group" column, clicking the right mouse button anywhere in a column checks/dechecks the entire column.
4. Clicking the list heading using left mouse button only checks the selected residues.
5. If there is no secondary structure information shown in the left of group name column, clicking left mouse button anywhere in the left of the group name column selects all groups in that chain; If there is secondary structure information shown in the left of group name column, clicking left mouse button on the structure info selects all groups in that structural element.

For the selected residues (highlighted as red):
a. Displaying only selected groups and clean others: hit "Enter".
b. Adding the selected groups to the view without hiding non-selected groups: hit "+"

Coloring molecules:

• Color individual groups by clicking each square under the color column in the Control Panel and select a color. This action will change the color only on the corresponding group that is in the same row as the "color" square. Clicking "cancel" in the color window, this will restore the default group color (CPK color).

• Color layers (whole molecules) by using the "Color" menu. (I.e. "Color: CPK or Type".) Color change may be restricted to "BS" (backbone and sidechain), "B" (backbone), "S" (sidechain) or "R" (ribbon). (See the figure below) This restriction method also effects the color change of each group.

• Useful Color Types

  CPK
  Cà white    Oà red    Nà blue    Sà yellow    Pà orange    Hà cyan    otherà gray

  Type
  Basic AAà blue, Acidic AAà red, Polarà yellow, Hydrophobicà gray. (These default colors can be changed in the preferences.)

RMS
To be selectable, this option requests that at least two proteins have been loaded, superimposed, and that a structural alignment has been generated. At this point, each amino-acid of the active protein will be colored accordingly to its RMS backbone deviation from the corresponding amino-acid of the reference protein (the first loaded). Dark blue means good superposition whereas red means bad superimposition. By default colors provide from a fixed scale, but you can choose a relative scale where the best RMS is dark blue, and the worse RMS is red by enabling the appropriate item of the preferences menu.

B-factor
The molecule will be colored accordingly to its temperature factor, from dark blue for low B-factor to red for high B-factor. In the case of a model returned by Swiss-Model, red means reconstructed. The highest B-factor of any backbone atom is attributed to all backbone atoms; the same is true for sidechains. By default colors provide from a fixed scale, but you can choose a relative scale where the best RMS is dark blue, and the worse RMS is red by enabling the appropriate item of the preferences menu.

Accessibility
Each amino acid is colored by its relative accessibility. Maximum accessibility is defined as being the accessible surface of an amino-acid X in a pentapeptide GGXGG in extended conformation. This is only an approximate scale, but perfectly sufficient to differentiate core amino-acids from surface ones. Dark blue color is attributed to completely buried amino-acids, whereas red color is attributed to amino-acids with at least 75% of their relative surface accessibility accessible.

Secondary Structure
A secondary structure detection will be performed immediately before coloring helices in red and strands in yellow. The rest of the structure is colored in gray. These default colors can be changed in the preferences.

Selection
This will simply color selected residues in cyan and non selected residues in dark gray. This is useful to quickly highlight the spatial position of some residues compared to the rest of the protein.

Layer
Each layer will be colored with its own color.

Chain
Each chain of the current active layer will be colored with its own color. Ideal to have a look at the arrangement of multimeric proteins.

Brief Operations:

Load a protein

Go to menu "File"à "Open PDB files"; or just drag the pdb file to the opened program window or the icon in the desktop [if you have already opened this program, this would open a second one]).

Display a trace of a protein

1. In the Control Panel, click anywhere in the "side" column using right mouse button. This would hide the side chains.
2. Go to menu "Display"à " Show CA Trace Only"

Measure and label a model:

• Click the "Measure distance between two atoms" button, following the instruction that appear above the model, click to select two atoms in the image, the distance between them will be appeared on screen.

• Click the "Measure angle between three atoms" button, pick three atoms that define the angle you want to measure (first pick the center atom, and then pick two atoms connected directly to it), SPdbV prints the bond angle both beside the picked angle and at the top of the view window. The three atoms need not be connected, so you can measure angles made by distant groups in a protein.
• Click "Measure w , f and y angles of the picked amino acid" button, then click on any residue, SPdbV displays the w , f and y angles. Hold down "Control" key and click this icon button, pick four successive atoms on a side chain. SPdbV reports the dihedral angle. With this feature, you can measure any dihedral angle, even arbitrary ones involving non-connected atoms.

Clear Labels:

You can remove the visible labels by going to (menu) "Displayà Label Kindà Clear User Labels".

Make Snapshot:

After you adjust the image in the view window in your favorite way, you could make a snapshot by going to (menu) Fileà Exportà Export Image, then select a directory and name the file, and click OK. This program will export the image as bmp file. (This hotkey for this manipulation is Ctrl-E)

Moving Technique: (move each molecule individually or only parts of the molecule)

Move each molecule individually: "Display"à "Show Layers infos" (Hotkey: Ctrl-I) to bring up the "Layers infos" window. In the "mov" column, check only the molecules which you do want to move. For example, if you only want to move molecule named "1hbg", the "Layers infos" window should look like the figure showing below.

 

Move parts of the molecule: In the "Control Panel" window, select the group(s) which will be moved. (Those selected should be colored be red in the group column in the control panel). Change "Move All" to "Move Selection" at the top left of the view window. (See figure)

 

Working with Ramachandran Plot window:

1. Load the protein pdb file.
2. Select the groups that will appear in the Ramachandran Plot window. (Before or after the Ramachandran Plot window is opened).
3. Choose the "Show Ramachandran Plot" item of the "Display" menu. Amino acid appears as a little cross with the exception of Gly that appears as a square. (Note that Gly and Pro can be hidden from the plot depending on the Preferences settings.) Placing the mouse pointer onto these little crosses (without clicking) will bring their name(s) to appear at the top of the Window. You could also distinguish these crosses by different color through coloring the selected groups.
4. Select the "Save Ramachandran" item of the "File" menu, this will write a tabulated text file containing the w , f and y angles of the currently selected amino acids.
5. The Ramachandran Plot window may also be used to alter the backbone: directly modify the f /y angles of a residue by dragging the little cross to its new location. The rotation around either of the f or y axis during this operation may be constrained by holding down the "9" or "0" key while moving the cross. By default it is the C-terminal part of the protein that will move, as a little 'C' appeared just below the help icon (?). To move the N-terminal instead, click on the 'C' for its changing into a 'N'. To move only a part of the backbone (not the whole backbone up to the C-terminal), first break the backbone after the last amino-acid that will move. This is done with the appropriate item of the tool menu.

Build multimer molecule from monomer by non-crystallographic symmetries

(In this example, we will build a capsid pentamer from the poliovirus protein monomer [2plv.pdb])

1. Open five copies of 2plv.pdb file. (Don’t rotate or re-orient any copy or click the right mouse button).
2. Select all residues in all layers by holding down the Shift key while invoking the "Select All" item of the "Select" menu.
3. Make the first layer active, click on the little text icon in the main display window, which will open the pdb file as a text file. Scroll down the pdb file to MTRIX lines, which represent three transformation matrices, and allow the non-crystallographic symmetries of the protein to be built.Note that there are three MTRIX lines for each 3 x 3 rotation matrix.

    4. Click on the first line of the first MTRIX record, this will load the transformation matrix into a
         dialog, simply click on OK, and the transformation will be applied on the current layer.
    5.  Repeat the similar manipulation for the rest of layers.
    6.  Color by layer and observe the full functional unit and observe which residues are making
         non-crystallographic contacts.

Build crystallographic symmetries

1. Open EDM preference dialog window ("Preferences"à "EDM…"). Make sure to check "Around CA" in "Display" section and "Draw Unit Cell".
2. Load the protein or nucleic acid pdb file.
3. Click on the little text icon in the main display window, which will open the pdb file as a text file. Scroll down the pdb file to CRYST lines. Click this line to load cell information.
4. Use the "Build Crystallographic symmetry" of the "Tool" menu to bring a window containing the symmetries operators to the front. Then click the space group header you want to apply to build the symmetries.
5. The original pdb file is then used to construct the symmetries and each symmetry will appear in a new layer whose name indicates which transformation was applied. Swiss-PdbViewer will try to construct the symmetries as close as possible to the current molecule.

Manipulating Electron Density Map:

Left and Right Arrow Key: Navigate along the peptide to look at the edm. (See control panel for the residue at which you are looking)

Up and Down Arrow Key change the sigma contouring value. (If you keep the Shift Key down at the same time, that will change the second contouring value)

Superimpose and calculate RMS:

1. Load at least two protein pdb files to superimpose. Display only their a trace. (The first loaded one will be the reference molecule)
2. Color them by layer or in any way that distinguishes each molecule from the others.
3. Select the "Magic Fit" option of the "Tool" menu. "RMS & Auto Fit options" apply to the superimposition.
4. For RMS value, use the "Calculate RMS" option of the "Tool" menu. The value will appear on the top the view window.
5. Bring the align window to front, and move the cursor onto one AA of the first protein, as you can see, it will blink in the view window, allowing you to immediately know where it lays in the protein. If you look at the bottom left of the align window, you will see a RMS value. If the value is high, a structural alignment needs to be generated.

Generate a structural alignment

1. Click on the name of the protein which was loaded second on the left of the "Align" window to bring this protein to the front.
2. Use the option "Generate Structural Alignment" on the "Tools" menu to so the alignment. This alignment would lower some RMS values.
3. Choose the option "color by RMS" from the "Tools" menu and look at the alignment window. Amino acids will appear in dark blue if they have a close correspondent in reference structure, and appear brighter when their RMS increases, up to be red if they have no correspondent in the reference structure.