AstexViewer™@MSD-EBI
(version 2) tutorial
Introduction
This tutorial is designed to understand the use and abuse of the AstexView™@MSD-EBI to view macromolecular structures and sequences. You will be taken through the basic control of each view (structure, sequence and graph), and then more advanced features associated with highlighting and display/manipulation of solid models. The initial parts of the tutorial cover very basic usage of the display, the later sections show how to use the viewer to analyze the structure and sequence information from the proteins. Even if you are used to other graphics programs it may be worth quickly running through the first section.
Start up the viewer by selecting this link. This will open a new browser window with the main documentation and start the download of the viewer applet. On completion of the applet download you should see a new window contain views for the coordinates and sequences of dihydrofolate reductase (7dfr and 8dfr). :
Structure view :
Sequence view :
Palette
The palette contains a number of buttons that can be clicked to change the view. Some of the buttons contain drop down menus with additional buttons and these are marked with a blue triangle at the right hand side. You will also see these buttons are grouped into three groups. The larger top group acts on the structure display and the lower set act on the sequence view, the separate select, brushing and magic lens buttons are more general and act on multiple views of the data. This applet will also provide some prompt text if you move the mouse over a pallet button and do not move it for about half a second. The help prompt text appears at the bottom of the applet within a status line. A number of pieces of information will appear within the status line while using the viewer such as the atom name while the pointer is within the structure view.
In the following tutorial any word in italics refers to a button or drop down button and text in courier font (plain font) is a question for you to answer. The questions are trivial, they are just to make you think about what you have just read.
All picking in the applet, including buttons that carry out an action, work by using a <LEFT-MOUSE> click action (press and release). If you only have one mouse button then use this one. Select the Show button by using a mouse click (press and release); this will open the drop down menu for the Show button that contains the buttons: Solvent, All, None, 7dfr and 8dfr. This drop down menu will stay open until you down one of the following - please do not click anything yet !:
You will see that the buttons for 7dfr and 8dfr have red text and a tick mark. Any button with red text and a tick is currently "active", and in this case these 2 structures are visible and are therefore "active". We will now hide the solvent atoms from the structure view.
Pick the Solvent button. What
happens to the structure display?
Some action buttons (7dfr, 8dfr) are toggle buttons, picking them multiple times will turn on/off the action they control. Not all the buttons on the palette are toggle buttons, for example the all and none buttons on the show drop down form a toggle pair so as to clarify their action.
Using the structure
view panel
The structure view shows the coordinate positions of the atoms for two molecules 7dfr and 8dfr as determined by the experimental technique X-ray crystallography. (20% of the current protein structure data was determined by the technique of Nuclear Magnetic Resonance NMR, and a small number by Electron Microscopy EM, the rest by X-ray crystallography). In fact the structures viewed are drawn as "half bonds" - that is, each atom type (nitrogen, oxygen, carbon, sulphur) dictates the colour of half a bond from this atom, the other half of the bond being coloured by the second atom in the bond. An atom position is therefore at the join/end of lines.
The display of the 3D coordinate bonds can be rotated by using a "virtual trackball" action: -
The display can also be translated using a virtual track ball motion. To translate the display in X/Y ordinates use the action of <CTRL><LEFT-MOUSE> and move the mouse in an x/y direction (where <CTRL> is the control key on the keyboard). In this case the molecule will follow the movement of the mouse.
(NOTE : if you have accidentally picked an atom
rather than an empty region on the display you will see the display
progressively magnify so that a small number of atoms (a residue) is at the
centre of the view and highlighted. To UNDO this - click on the palette button Zoom
out which is the third button down and the display will return to the
previous whole screen view.)
The sequence view shows the order of the residues within the protein sequence using letters that uniquely define each amino acid, and coloured boxes that are defined by a residue property. The initial view will have the sequences positioned so that the N-terminal residues are approximately central to the sequence panel. Notice that 3 of the sequences have a double insertion at the beginning , the fifth sequence has a triple insertion at the beginning. The right hand edge of the sequence panel has the sequence display progressively compressed, initially so that the character label is missing, and finally with coloured boxes shown as thin lines. This style of display is known as the hyperbolic view; a linear view is also available.
Using the scroll bars
You will see two scroll bars for the sequence display - the left-right bar is at the top of the sequence panel and below the structure view panel and the up-down scroll bar is to the right of the sequence panel. The left-right scroll handle is currently placed at the left-hand side of the scroll bar, you will use this to move the sequence display as follows:
This click and right drag of the scroll bar handle will scroll the sequence display so that when the mouse scroll handle is at the far right of the sequence panel you will see that the end of the sequences are approximately centered in the view. Since there are only 5 sequences, the up-down scroll bar is not useful (yet).
Using a virtual trackball
You can move the sequence using a virtual track ball action, like the structure view. This virtual track ball action only changes the left-right position of the sequence, it does not change the sequence in a up-down direction.
This click and drag action will move the sequence so that it follows exactly the motion of the mouse pointer only in a horizontal direction.
What difference is there between using the
scroll bar handle and the virtual track ball action ? (hint - how fast is the
display moved, and what direction ?).
Which method would you use to move quickly
from the beginning to the end of the sequence ?
Picking the structure and
sequence views
This section discusses what happens if you pick an "object" in either the sequence or structure view. An object is any thing that is displayed within the respective panels, such as a 3D atom position (the join or end of lines) or sequence entry (a letter). Picking any empty part of the sequence or structure views has no effect.
First it is necessary to discuss the meaning of view-context. The view context defines how much or what sort of thing you expect to see and how you see this information; essentially - what scale the display is set to and how is the data drawn. The currently structure view is for the whole molecule (if not use the zoom out button), and so the structure view context is "whole-molecule". Picking any object within the structure or sequence view will change the context of the structure to that of "residue-context". The sequence view has multiple view contexts as well, but we will cover these later.
Picking the structure view
Please pick any "atom" in the structure view, this is either at the join of two lines or the end of a line - in fact just click anywhere near the centre of the structure view panel where there are lots of atoms, you will hit an atom! A number of changes will occur to both the structure and sequence view:
Picking of the sequence view can have two affects because there are more sequences displayed than structures. If you pick the sequences labeled 7dfr or 8dfr then the viewer will update both the sequence and structure views, if you pick the sequences for 3dfr, 4dfr_A or 4dfr_B then only the sequence view will update. Please pick a character (residue) from the top sequence in the sequence display labeled on the left with "7dfr".
Try picking a number of different atoms in the structure view and sequence characters in the sequence view. Get used to the change of display and try and understand what happens to the sequence and structure displays when picking objects. Note that the structure display does NOT update if you pick the sequences 3dfr, 4dfr_A or 4dfr_B.
How many structure view contexts are
there?
How is highlighting shown in the structure
view?
How is highlighting shown in the sequence
view?
What happens to the highlighted residue in
the sequence and structure view when you use the Zoom Out button?
What happens if you pick and insertion
"-" character in the sequence view?
This completes the basic picking use of the mouse and mouse button picking and use of the palette buttons. We will visit the use of graph picking and brush highlighting later in the tutorial for interactive highlighting of features in all the views.
Visibility of displayed
molecules and controlling what you see
Changing the structure view
You will have already used the show drop down button to turn off the display of the water molecules, we are going to change visibility of each structure, then create different displays (surfaces and ribbons) and finally how to control the visibility of all the types of display. If you are continuing with the tutorial from the last lesson please return the main structure view to the molecule context using the Zoom out button on the palette. You should see two structures in the centre of the structure panel superposed.
Molecule Visibility
Click on the Show button drop down button, and then click on the button marked 8dfr and you will see that this structure is now hidden from the coordinate panel. If you open the Show drop down menu again you will see that the button marked with 8dfr is now written in blue text without a tick - thus its activity is false and the structure is not shown. Click somewhere else in the palette panel and the show drop down will close without any changes.
Solid model views
The viewer has a number of display types that are collectively known as solid model views. There are 4 buttons dedicated to the generation of solid model views; 3 drop-down buttons that control the display type for protein atoms, Nucleic acids atoms and Ligand atoms. A 4th button allows you to generate complex display types and to modify the existing solid model views.
The button Protein is used to create solid surfaces for proteins, the NucleicAcid button is not visible in this tutorial as there are no nucleic acid residues in these molecules, and the Ligand button creates solid surfaces for all ligand/ion atoms. We are going to create a surface for the protein molecules and a ribbon cartoon representation. Pick the Protein button and a drop down list of 8 different display types + reset will open. You will see that the default display of Line is already selected as all the current molecules are drawn in a line style. To draw a solid surface click the drop-down button SolidSurface. There will be a pause of about 10 seconds while the computer first calculates this display and then a blue solvent surface will be shown. If you now open the Protein drop-down list again you will see that the SolidSurface option is now highlighted – you can turn this display off again by picking the same drop-down button. Notice that if you turn this on for a second time the surface will appear immediately. This is because it has already been calculated, and so will just be made visible. The reset button at the top of the three drop down button lists are used to delete the graphical object complete, whereas a second click of a sub-button only hides the solid model view. This allows you to modify some property used to generate a solid model and then redraw it using the new property. For example, the solid model view colour (not for surfaces) is taken from the atom colour, and the extent of the solid model view is defined by the atom selection.
All display types are only visible when the molecule is shown – refer to the
section on molecule visibility.
How would you turn on/off the solid
surface display of 7dfr
The 3 pull-down buttons for protein, nucleic acid and ligand atoms provide a way to generate simple whole molecule views. For example you could display the protein with a surface, the DNA using a cartoon and the ligand as a stick model. Later in the tutorial we will use the selection palette to create different display types for parts of each molecule; at this stage the applet has created a solid model view for all atoms as no atoms are currently selected.
The Solid Model button opens a dialog box that allows the creation of
new surfaces and the ability to modify existing surfaces. There are 4 tab panes at the top of the
dialog, the first and default tab allows the selection of atoms, the second tab
all the creation of graphical solid models, the third tab can modify these (and
those generated from the simple displays), and the fourth the lighting model.
This section will teach you how to use the basic built in colour and highlighting selections; user-defined colours, highlighting and display is covered later. If you are continuing with the tutorial from the last lesson please return the main structure view to the molecule context using the Zoom out and Show buttons on the palette and remove any ribbons, graphs and surfaces using the appropriate buttons. You should see two structures in the centre of the structure panel superposed and the sequence display with 5 sequences coloured by the default discrete polarity scale.
There are two colour buttons on the palette, one modifies the colour of the structure view and the second controls the colour used on the sequence view. The Colour drop down allows 13 different colour schemes, 2 change the background colour of the structure view, 6 represent single colours, and the remaining five use colour to represent a single property (atom type, temperature factor, sequence position, chain number and the sequence colour). Click on the Colour drop down and select the Bvalue button; this will change the displayed structures so that they use a red to blue colour scheme where red = large Bvalue (hot) and blue = small Bvalue (cold).
What difference is there between the
Bvalue range for 7dfr and 8dfr?
The Chain button on the Colour drop-down will colour each chain differently, though note that 7dfr and 8dfr only have single chains so each molecule in this example will be coloured green and yellow. The Sequence button will copy the current colour scheme from the sequence display to the structure display. Pick the Sequence button and the structure view will display the molecules using the sequence colouring, we will use this later to swap structure and sequence information. The 6 single colours are used in conjunction with the atom selections so have little use with regard to whole molecule display.
What colour scheme is used for the
structure display if the default Sequence colour is added to the
structure?
The colour of the solid model views (not including the surfaces) are taken from the atom colour when the solid model view is generated.
Why are the surface colours not
taken from the atoms ? hint – think about what a surface represents and how it
is calculated.
The graph drop down button allows the generation of predefine graph types as well as graphs of data sent to the viewer as attributes. Pick the graph drop down button, and select the Rama. button while only the stick diagram of 7dfr is shown. This will produce an additional window showing a Ramachandran plot for the 7dfr structure only with the colours : blue = glycine, green = proline and red = rest. Close this plot using the [X] window button at the top right of the Ramachandran graph window.
What happens if both molecules are visible
when the Ramachandran plot is created?
What happens if no molecule is visible?
What happens if a Ramamchandran plot
exists when you create a new plot?
Delete the Ramachandran plot when you have finished this section using the [X] window button on the Ramachandran plot. We will re-visit the generation of graphs and highlighting information on these graphs later in the tutorial.
You probably have noticed that 7dfr and 8dfr are superposed within the structure and sequence panel. When you use the viewer from our search systems you will often get multiple hits loaded within the viewer. We wish to show how these molecules compared by both structure and sequence, so these are always loaded aligned to allow various comparison functions to highlight relationships. Of course it is possible using the search system to request views of structures and sequence that have no relationship at all. This tutorial example uses the structures of 7dfr and 8dfr and additionally the sequences of 3dfr and 4dfr to demonstrate the functionality. The tutorial you are running also has loaded the structure of insulin (3ins) and of course this structure and sequence certainly does not align with dihydrolate reductase.
Groups
This gives rise to what we define as groups. A single group of molecules is define as those proteins that align by sequence (>40% ) and align by structure (< 2 Å & > 40 residues). If multiple molecules are loaded into viewer which do not conform to these limitations then a separate group is made.
The first button on the palette is Group, and picking this result in a drop down menu containing buttons dfr and insulin. These two buttons access two separate groups, in this case the set of molecules { 7dfr, 8dfr + sequence 3dfr, 4dfr_A, 4dfr_B } and the set of { 3ins }.
Select the group insulin and you will get the structure and single sequence for insulin (3ins). Use the Show button to hide the solvent and then try out the ribbon and surface generation tools. If you have forgotten how these are used then refer back to this section to use these features.
What do you see when you display the
ligand surface for insulin?
Use colour by chain to find
out how many chains this molecule has
What colour scheme is used for the ribbon
display?
These two groups in the tutorial example are very simple, you should be aware that the grouping carried out from a query request can produce very complex sets of proteins. The grouping is carried out automatically on our server when the results of a query are generated, the alignment by structure and sequence is based on the chain structure of the query results resulting in many possible combinations of alignment. For example, are 4 possible groups than can be defined from the alignment of a single myoglobin and a single hemoglobin molecule as the latter contains 4 chains and visually these different groups look identical but result because the myoglobin molecule aligns with each chain.
The basic usage of the sequence display has already been covered; we will now look at the tools to highlight this functionality. The sequence panel is designed to display sequences of character strings (the sequence) as will as marked points (active sites) and links between different parts of the sequence (disulphide bonds).
Please select the first group dfr that shows the five aligned sequences of dihydrofolate reductase.
Sequence annotation
We will first try the Seq.Show. button, this has two options to show Active site and disulphide information. Use the Site menu button from this drop-down button to mark on the active site residues. "#" characters will be added to the display in five rows below the main sequence information.
Why are there only site marks for
sequences 7dfr and 8dfr?
These marks show the residues that are within 4Å of a ligand and can be picked using the mouse pointer. Try picking one of the "#" marks to update the sequence and structure view. Turning on the disulphide display using the Seq.Show. drop down and Disulphide button
How many disulphide bonds are there in
dihydrofolate reductase?
Change to group insulin using the Group drop down so that the insulin molecule and sequence is displayed. Now pick the Disulphide button again of the Seq.Show. drop down and lines will connect the residues that form disulphide bonds in the structure. Multiple sequences are moved apart when this disulphide information is shown to make room for these join lines.
How many disulphide bonds are there in
this insulin molecule?
Sequence display styles
Please change the group back to group dfr so that you see the dihydrofolate reductase molecules; notice that any Seq.Show. settings are reset on changing groups.
The Seq.Style. contains four options that control the display of the sequence panel. Group and Hyperbolic are currently active. The buttons Group and Block form a pair of toggle buttons and Linear and Hyperbolic form a pair of toggle buttons; they change the sequence view context. Turn on the Site marks using the Seq.Show. drop down and then change the display style (Seq.Style) to Block. You will now see that the site marks are placed just below the sequence they correspond to.
The sequence display is not long enough to
see 2 of the sequences in Block mode, how would view the hidden
information?
The Group/Block pair of buttons therefore change the sequence display so that sequence strings and their annotations can be grouped together in different ways. Change the display style between Group and Block to make sure you see the difference when the site marks are active.
The Linear and Hyperbolic buttons on the Seq.Style drop down changes how the sequence panel is drawn. Change the view context to between hyperbolic and Linear. You will see that in Hyperbolic display shows the entire sequence all the time but the edges are squashed. The linear display keeps the sequence display the same resolution all the way along, and the ends scroll off the edges of the display.
Return to the insulin group and
display the disulphide bonds. How many disulphide bonds can you see in the
hyperbolic view?
How many disulphide bonds can you see at any
one time using the Linear view?
Repeat this with the site marks for
insulin.
Sequence colouring
Please set the group to dfr, and return colours and highlights to their defaults.
There are 11 different colour schemes that can be used to highlight properties on the sequence display, the default is Residue which uses a discreet polarity scale (acid = red, glycine = orange, polar = green neutral = yellow, histidine = pale blue, basic = blue) to colour the sequence. The Charge button will highlight just the acid and basic residues while Hydro. use a continuous red to blue scale based on residue hydrophobicity.
The Consensus button colours multiple sequences using a consensus sequence alignment scale between blue = constant (cold) to red = variable (hot) range.
A red background is used where there is no
sequence identity; therefore what effect does an insertion (shown as
"-") have on the colour scheme? (hint - look at the first residue)
The colour scheme Structure allows the current structure display colour scheme to be placed on the sequence where the colour is picked up as the modal value over all the atoms of a residue. The default colour of the structure is by element type, and since all residues contain mostly carbon (green) then the use of this button with the default structure colour scheme makes the entire sequence green.
Why don't the sequence colours for 4dfr_A,
4dfr_B and 3dfr change when using colour by structure?
How would you colour the structure by
consensus sequence alignment? (hint - look at the colour button drop
down menu)
More Similarity and
Difference
We will now use the Colour and Seq.Col. drop down buttons along with the similarity analysis buttons to highlight difference and similarity within both the sequence and structure. If you are continuing with the tutorial please select Group = dfr, make sure both structures are displayed, change the structure colouring to Element and the sequence colouring to Residue. You should see two structures and five sequences aligned and superposed.
Similarity in structure is shown using the Similarity drop down button, please pick this button and select the Col.Dist. button. This will colour all the displayed structure using a red to blue colour range where this colour is dependent on the distance to the nearest CA (from the CA atom) of any other displayed structure. Each atom in a residue is coloured the same based on this CA-CA distance, and blue (cold) is used for small separations and red (hot) is used for large distances or unmatched CA atoms. The Col.Freq. button uses a similar red to blue colour range but is based on the number of structures that have a CA atom of similar position to a target CA atom; this option is sensible where many structures are overlaid.
Colour the sequence using this structure
alignment colour scheme
Some of the sequences do not change
colour. Why?
The Bvalue for an atom is the experimentally derived information that indicates (in part) the amount that atom moves during the crystallographic experiment. It gives some idea of the dynamics of the structure on an atomic basis.
Colour the structure by Bvalue. Why
is the outside of the structure red and the inside blue? (There are two main
reasons).
How would you colour the sequence by
"modal" residue Bvalue?
What does this show given that the
sequences are aligned?
If Seq.Col. drop down and consensus button is used to colour the sequence, then this colour scheme can then be dropped onto the structure so that the atomic bonds are coloured using the sequence alignment information.
Four different graphs can be produced based on any displayed molecular structure. These graphs show different structure related information and open a separate window which can be closed using the [X] window button at the top right of the respective plots. Please make sure that the default display is shown, with Group = dfr and the atoms are drawn using the Element option of the Colour drop down. Details of using the basic graph control can be found here.
Use the Show drop down button to just show the structure 7dfr.
Ramachandran Plots
Pick the Graph drop down button and the Rama. button to draw a Ramachandran plot of the molecule 7dfr. A new window will open with symbols to show the values of phi and psi. (Blue = glycine, green = proline and red = rest). Pick a symbol on this graph. You will see the following effects:
Try a number of different points on the graph, and then pick atoms and residues from the structure view and sequence view. You will see that the Ramachandra graph will also be labeled if either the structure or sequence view is picked.
The colour scheme used for the Ramachandran graph (blue/green/red) is used if the molecular structures are coloured by Element. If the colour scheme of the structure is not Element then the current structure colour will be transferred to the points in the Ramachandran graph.
Using this information create a Ramachandran
plot for 7dfr coloured by consensus sequence alignment.
Why are there no blue points in the
reverse turn region ?
Bvalue and Omega Plots
The Bvalue plot displays the mean Bvalue for each residue plotted as a function of the residue number. The default colour scheme used (when the structure colour scheme is element) is defined by the molecule number. Different colour schemes are set by colouring the structure, but note that since the graphs are "chain" based, the colour used will be the mean colour over an entire chain.
Select Graphs drop down and the Bvalue button and a plot will appear. Repeat to produce a graph of Omega as a function of residue.
You will now have 3 graphs open on the display, drag the Omega and Bvalue plots to other parts of the screen, so all three can be seen. Pick any graph and you will see that all of the Structure, sequence and all graphs will be labeled with the point picked.
What does it say in the Ramachandran plot
if you pick the first sequence entry of 7dfr? Why?
The Multiple plot
The multiple plot is a dynamic graph that shows 4 different properties at one time, and is used here to show the phi and psi torsion angles, the omega angle from the peptide bond, and the mean temperature factor of all the atoms in a residue. The X and Y ordinates of the graph are used for phi and psi – just a in a Ramachandran plot, while the temperature factor is shown using a colour range (red to blue) and the Omega value by the size of each graph point.
At the top of the plot are 4 double slider bars. You can drag the left and right slider bars using a click and drag action, or both at a time with a click and drag action of the space between the slider bars.
What do the slider bars do to the
plot ?
How would you know if there was a correlation
between the Ramachandran angles and the temperature factor ? Is there a
correlation ?
The single reset button returns the plot to the initial state.
The CA-CA distance plot
The CA-CA distance plot is produced for the first displayed molecule in the structure view using the Graph drop down and CAdist button. This plot is a dumb plot and cannot be picked and does not highlight when any point is picked.
Atom selection defines the action of changing the structure display so that only a subset of atoms is displayed, coloured or drawn with different solid model representations..
Open the Selection palette with the select button and a separate window will open with a single button and some labelled control marks "[-]- 8dfr" and "[-]- 7dfr" and "[+]-( )", "[+]-( )". These are references to the molecule names (open) and chain names (closed - names are blanks). Unfold the chain from 8dfr fold using the top [+] mark using a left mouse click. The residue information will unzip to fold out this level of hierarchy. Each [+] box unfolds a higher level of hierarchy and a [-] folds up a level of hierarchy.
Use the [+] and [-] marks to fold and
unfold chain, residue and atom information.
Picking a label will select this object. Select residue "16 : ILE" of the structure 8dfr. The object name turns red showing that it active. Look closely at the structure view panel and rotate it with the virtual track ball action to find this residue which has been highlighted with yellow boxes.
How would you colour this residue cyan.
How would you draw solid model spheres on
this residue.
The single button is used to select those residues that are in contact (any atom less than 4A) with the ligand. This allows these residues to be annotated by colour or using one of the different solid model displays.
What happens to the atom/residue selections when you select the chain name "( )" for 8dfr?
This palette is a hierarchy view of the data, and selecting a lower level of hierarchy propagates this selection up the hierarchy. This allows, for example, the resetting of the residue selection using the chain selection.
We are now going to select a range of residues, first set the selection for 8dfr to "unselected" by picking twice the 8dfr label; so that all objects are blue. Select residue "10 : VAL" by picking the name - it should go red. Now move to residue "30 : GLU" and <SHIFT> <LEFT-MOUSE-CLICK> this residue. All residue names from "10 : VAL" to "30 : GLU" will turn red.
Leave these residues selected and repeat
this action for the range "5 : ASN" to "35 : GLN" (you may
need to scroll the view with the scroll bar at the right of the select panel).
What happens? Now create a cartoon solid model for these residues.
Highlight the ligand using the selection
view of the data.
Hide all the solvent for 7dfr using
the selection data view.
Note : It is possible turn the display off for a
whole molecule from the Show drop down button on the main palette, or
use the Select palette. It is highly recommended that for general
show/hide of each molecule that the Show drop down button is used for
this and not the select palette. Visibility set using the selection
palette is atom based, so the structure display is significantly slower than
when set by the show button which is molecule based.
Brushing is the term used to define the action of automated highlighting of information as the mouse is moved over any of the view panels. That is, without the user clicking a mouse button or pressing any keyboard button the application returns information about selection within the connected views. The viewer contains a number of different views of the macromolecular data, structure, sequence, selection and derived graphs. Each of these views show macromolecular data in different ways, but each data view is linked by the basic organization of the macromolecules.
The computer screen you are using is a 2D surface, so the brush that can be passed over a panel is therefore a 2D shape that encloses some data points. Within the sequence view you get a rectangle, and in the graphs it is oval, and the structure provides a square.
Reset the view so that you see the two molecules with the default colouring. Turn on brushing; using the button labeled brushing. A number of different visual effects result as the mouse cursor is moved into each of the panels, warning - things can get a bit "busy".
Note : The brushing effects are
"computationally expensive". That is, if a large number of molecules
are loaded, or these are large then there may be significant pauses on a slow
computer.
Mouse movement within sequence panel
Mouse movement within a graph panel
Mouse movement within the selection palette.
Mouse movement within the structure panel
You should hide the molecule 8dfr and create a Ramachandran plot from the remaining visible molecule 7dfr. You now have 3 panels; structure, sequence and the Ramachandran plot. Move the mouse over each panel and observed how highlights appear in other panels. The effects can be rather busy (lots of information returned) so this option can take a little getting used to.
Highlight the residues within the
structure and sequence views in a helical conformation using the Ramachandran
plot.
You will find that the selection oval is not quite big enough to do this, so we will increase the size of the selection oval. While the cursor is in the Ramachandran plot, hold down the <SHIFT> keyboard button and the <LEFT-MOUSE> button while dragging the mouse cursor in any direction. This <SHIFT> mouse drag action will edit the size of the selection oval. You will notice that the drag in "x" and "y" changes the oval's x and y extent separately. When the oval is large/small enough let go of the mouse and keyboard buttons. If you happy with the size of the selection oval then:
Highlight all the reverse turn residues.
What happens to all the selection marks
when you exit a panel ?
It would be nice to hold onto a selection so that each view can be studied in different panels. We are going to lock a selection made using the Ramachandran plot so that you can view the structure and sequence with the helical residues highlighted. Move the cursor to the Ramachandran plot and select helical residues, you will see that the structure and sequence views have been highlighted. Now pressed the <SHIFT> button on the keyboard - and NO mouse button. Pressing the <SHIFT> button locks the current selection; you can now move the cursor out of the Ramachandran view and into the structure panel. Let go of the <SHIFT> key. Use the virtual track ball to look at the selected residues. Now move the cursor into the sequence panel and pan the sequence view with the scroll bar handle.
The <SHIFT> keyboard key locks a selection from the sequence or graph view so that other view panels can be manipulated. You need only hold the <SHIFT> key down until the mouse point has left the panel with the locked selection.
Using the description to change the graph
selection box, change the sequence selection window so that only a single
residue from all the chains is selected at any one time.
Generate a Ramachandran plot for both 7dfr
and 8dfr. Using the single residue selection window in the sequence panel,
traverse the sequence. What do you notice about each pair of points highlighted
in the Ramachandran plot? (Hint the structures and sequences are optimally
aligned)
Next, open the select palette using the Select button. The select palette can also be used to highlight the structure, sequence and graph views, in this case selection is based on the hierarchy of molecule/chain/residue within the selection palette. Open up 7dfr so that you can see the residues, run the mouse cursor over the residues and then over the segment name and molecule name.
Selection is NOT by area in the select view, how is it defined?
Magic Lens
The magic lens acts on all the views and can highlight hidden information set in the attributes – though the default is the ligand and active site. The aim of the magic lens is to provide a moving window over the structure view that allows the user to observe other information while retaining the coordinate view context. Make sure the brushing is off.
What residues are shown highlighted
in the structure view ?
What happens when a surface is
displayed while using the magic lens ?
The graphs and sequence view show the active site residues within the magic lens sorted so that residue closest to the pointer is at the front of the display.