Short Manual for Quick Reference
(Use "Tab" to change the currently active tool between B, C, D)
(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.
- 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 groups 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 groups show color.
Some manipulating tricks:
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 "+"
Cà white Oà red Nà blue Sà yellow Pà orange Hà cyan otherà gray
Basic AAà blue, Acidic AAà red, Polarà yellow, Hydrophobicà gray. (These default colors can be changed in the preferences.)
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.
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.
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.
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.
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.
Each layer will be colored with its own color.
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.
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
Measure and label a model:
- 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.
You can remove the visible labels by going to (menu) "Displayà Label Kindà Clear User Labels".
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:
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])
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
Build crystallographic symmetries
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:
Generate a structural alignment