EBI-AstexViewer molecular sequence & structure viewer

AstexViewer(TM) is a trademark of Astex Technology Limited

• This software includes code developed by Astex Technology Limited, Cambridge Science Park, Milton Road, Cambridge, UK and has been modified by the Macromolecular Structure Database Group of the European Bioinformatics Institute under licence from Astex Technology Limited.

Please refer here for conditions of use of the viewer

Tool usage for the viewer is found here

General usage of the viewer is described here

AstexViewer™ has been supplied as it may prove useful to the structural biology community. No warranties of any kind are provided or implied. You may use the AstexViewer™ software as provided herein for any purpose subject to the terms and conditions under which the Macromolecular Structure Database Group of the European Bioinformatics Institute may make this software available to you and the following additional terms and Conditions of Use imposed by Astex:

1. Astex hereby grants the user a personal, non-transferable and non-exclusive right and licence to use the AstexViewer™ software supplied herein. The user is not permitted to copy, modify, create a derivative of, reverse engineer, reverse assemble or otherwise attempt to discover any source code, sell, assign, sublicense, distribute or transfer the AstexViewer™ software. Any attempt otherwise will automatically terminate any user rights to use the AstexViewer™ software.
2. The user is not permitted to repackage the AstexViewer™ software for inclusion in other packages without the prior approval of Astex.
3. The AstexViewer™ software is provided "as is" and Astex makes no warranty as to its use, performance or results which the user may obtain using the software.
4. Astex makes no warranty, express or implied, as to the merchantability, non-infringement of third party rights, or fitness for any particular purpose.
5. In no event will Astex be liable to the user for any consequential, incidental or special damages, including any lost profits or savings, or for any claim by any third party.
6. Astex is under no obligation to maintain the AstexViewer™ software provided herein or to respond to requests for information from the user.
7. A notice to ‘Astex Technology’ must appear in any copy that you are permitted to make under the terms of this agreement. If you use the AstexViewer™ software on a publicly accessible internet site the user shall include the Astex company logo on the site as well as an acknowledgement of the origin of the program.
8. For any publication arising from the use of the AstexViewer™ software, a reference to Astex Technology as the originator and author of the AstexViewer™ software should be given as:
1. Michael J. Hartshorn (2003) " AstexViewer™: An aid for structure-based drug design", Journal of Computer Aided Molecular Design (in press).

Further information on AstexViewer™ is available at www.astex-technology.com

The search system produces groups of proteins based on whether the proteins can be aligned by structure and sequence. The hit list from a search is analyzed to group together all proteins that can be superposed by structure and sequence and respective alignment algorithms are used to carry this out. The group proteins are handed to the viewer as aligned structure/sequence. Each drop-down element under the group button is therefore a view of each of these group of aligned structure/sequence.

The group drop down button is only available if more than 1 group has been supplied to the viewer. The initial group displayed is the first group containing visible molecules. Selecting a different group will result in changing all the structures and sequences displayed to that designated by the grouping from the search. If a group is selected is that contains no visible molecules (selected from the search results) then a warning is added to the base of the structure panel. The view of the structure and sequence is reset on picking a group drop down button even for the current group. The user cannot change the group designation within the viewer as this is a server side designation.

The show drop down button will contain a list of buttons of all the currently loaded structure names and "none" + "all". Picking a selected drop down button will toggle (hide/show) the structure view of that name. The all and none show drop down buttons will turn on/off respectively the visibility of all the structures. The names on the drop down buttons will be changed as structures are loaded/unloaded as the new-loaded structure is added to the show list and the unloaded structure is removed.

The zoom out button will scale the structure view so that all the molecules in the display will fit within the structure view panel. If the view is already zoomed out then the view is reset so that the displayed molecules fill the structure panel otherwise the view will fly/snap from a residue focus to the full molecule focus.

The surface drop down button is used to calculate and display surfaces for loaded molecules. The first button on the drop down list is calculate, this will submit a background process to calculate separate surfaces for each molecule and each ligand of each molecule. The progress of the calculation is indicated by the status line at the bottom of the structure viewer and on completion there will be no text written at the base of the display. Note, that since a surface is calculated separately for each ligand and macromolecule there will be two calculations per molecule. The ligand surfaces are calculated first. Additional use of this button will check if any sufaces need to be calculated, and only calculate those not yet available. This will be the case if the user has changed groups, or loaded additional structures within a large group.

The ligand drop down button will toggle on and off the display of ligand surfaces for the currently visible molecules, and the protein drop down button will toggle on and off macromolecule surfaces for the currently visible structure. It is not possible to display a surface if it has not yet been calculated.

Since the protein and ligand buttons will only display surfaces for visible molecules it is possible to change the displayed surfaces by changing the coordinate visibility first (show), and then reusing the protein and ligand drop down buttons.

The ribbon button will generate ribbons for all loaded molecules and then display only those with visible coordinates. Additional use of the button will toggle on and off the ribbons. Each use of the ribbon button that turns on the display will check for uncalculated ribbons, this will be the case if the user has changed the group or loaded additional molecules within a group.

The mark ligand button will highlight using wide bonds all the ligand residues for the currently visible molecules. Ligand are all non-protein/non-nucleic acid/non-water residues.

The mark site button will highlight using wide bonds all the macromolecule residues for the currently visible molecule in contact with ligands. A contact distance of 4.0A is used.

The colour drop down button is used to change the colouring of the currently displayed molecules.

1. Element will colour atoms so that carbon = green, nitrogen = blue, oxygen = red, sulphur is yellow.
2. Bvalue will colour the atoms using a colour scale (red – white – blue) based on the Bvalue for each atom. Red is used for atoms with a large Bvalue, and blue for atoms of low Bvalue
3. Chain will colour each chain of each molecule a different colour.
4. Sequence will colour the all atoms of a residue the same colour as the equivalent residue in the sequence table. For example, if the sequence is currently coloured using sequence alignment consensus then the colour of each residue within the sequence will be used for all the atoms of a residue in the structure.

The similar drop down will carry out a similarity analysis for all overlaid molecules currently displayed.

1. Join will generate a white line segment to join all CA atoms of different molecules within 1.5A of another molecule
2. Col.Freq. will colour each molecule residue by a normalised frequency value. The frequency is defined as the proportion of the currently displayed molecules that residue is in close contact with (1.5A). This is probably of most use when multiple (more than 2) molecules are overlaid. The colouring will give a concensus similarity of residue position over all the molecules. A blue residue is most similar over all molecules, and a red residue is most dissimilar.
3. Col.Dist will colour each residue of the displayed molecules with a colour proportional to the minimum distance to other equivalent residues in other molecules. This display is of most use when viewing two molecules, and blue atoms are close, and red atoms are 1.5A or more away from an equivalent residue.

The graphs drop down will contain a list of possible graphs that can be drawn based on the currently visible molecules.

1. Rama will display a Ramachandran plot of the currently visible molecules. The default colouring is for glycine residues to be drawn blue, proline residues to be drawn green, and all other residue type to be drawn red.
2. Bvalue will display a line graph of mean Bvalue/residue for each residue of a macromolecules; for all displayed macromolecules. Each line graph, for each macromolecular will be draw in a different colour.
3. Omega will display a graph of protein torsion angle omega for each residue of the protein. Each displayed molecule will result in a graph line of different colour.
4. CAdist will display a CA distance matrix for the first displayed molecule. The distance matrix will be contoured so that blue is a small separation and red is a large separation; the highest contour drawn represent a separation of 25A.

The sequence style drop down will change the sequence display type between 5 different modes. The Block and Group styles are a toggle pair and the Linear and Hyperbolic are a toggle pair, and Highlight is a toggle on and off of a point brushing of the graphs and sequence.

1. Group will arrange the sequence information so that all the sequence strings are displayed together, and the active site markers are arranged together in groups.
2. Block will arrange the sequence information so that sequence strings and site information pair is arranged together for each sequence.
3. Linear will display the sequence information so that a flat scrolling display is used.
4. Hyperbolic will display the sequence information using a tanh function so that the centre as if the sequence is drawn on a cylinder.
5. Highlight provides a rectangle within the sequence view and an ellipse within all the graph views that follow the mouse cursor when it is moved within the respective data views. As the shape is moved all the equivalent data points within the structure view and graph views are highlighted to give an interactive paintbrush for the data.

1. The size of the rectangle/ellipse can be changed using a <SHIFT> <MOUSE-CLICK-DRAG> action. That is, while holding the <SHIFT> key down and the mouse button down the mouse should be moved. The highlight shape will be stretched in x/y as the mouse is moved away from the initial starting click point. The sequence rectangle size has discrete size values that is given by the size of a single sequence character width and height. The minimum size is a single sequence and residue. The ellipse in the graphs can have any value greater than 2 units of the graph. Different ellipse sizes can be set for each graph view.
2. On leaving a graph/sequence view all highlighting is removed by default. If the user wants to retain a particular highlight (ie alph-helix from the Ramachandran) and examine this in detail within, say the structure view then use <SHIFT> while moving the mouse. Holding the <SHIFT> key down locks the current highlight and allows the cursor to be removed from the view.

The sequence colour button allows the sequence to be coloured using a number of different colour schemes.

1. Residue : A default residue colouring
2. Charge : ASP/GLU = red, ARG/LYS = blue, HIS = cyan, rest = grey
3. Hydro : A colour range (blue – white – red) based on a hydrophobicity scale. Red = hydrophilic, Blue = hydrophobic
4. Consensus : A colouring based on the consensus alignment over all the sequences displayed using a colour range from blue – white – red. Blue is used for columns with no residue type variance, and red is used for columns with highly variable residue types.
5. Structure: The current colour scheme of the residues within the structure view is superposed on the sequence. Only sequences with a current equivalent structure will be changed.

Adds additional information to be added to the sequence display.

1. Disulphide will add lines between cystine residues that are connected by a disulphide bond within the coordinate structure
2. Site will add a # mark for each residue that is in contact with a ligand in the coordinate structure

The viewer is designed to display coordinate and sequence information from macromolecules and small molecules. It can also display graphs of data in a number of different ways. The viewer is designed to allow coordination between the different views, any pick or highlight in one view will highlight the equivalent reference point in the other views.

1. Picking atoms, sequence residues or graph point will update all views
2. Colour can be queried from one view and dropped onto another view

The Viewer is run as an applet to display the results of a search. It therefore has a number of properties that result from this use.

The result of a search of the DB can result from in a list of molecules, these molecules are grouped on whether they align both by structure and sequence. A group of structures are those that can be superposed by structure and sequence. A search of the DB can therefore result in one or more groups of structures to display, and the viewer has a drop down list of buttons to view each of these independently.

The user has the ability to select structures from the result list that they wish to see in the viewer. This visibility list is passed to the viewer and defines the default display of structures when each group is viewed. The show button in the viewer can be used to turn on and off visibility of structure within a group.

Since it not possible to know the resources available to a client process, the resources taken by the viewer is controlled by limiting the number of structures that can loaded at any one time. The viewer will only load a maximum of 8 coordinates sets at any one time, and loading an unloading of structure is automatically controlled by picking the list of names on the sequence panel.

The main viewer consists of a single window that is divided into 3 panels (figure 1). The left-hand panel contains the palette of tools, the right-hand top region (black background) is the coordinate viewer, and the bottom is taken up with the sequence viewer. If the viewer size is adjusted then the palette width and the sequence height remains constant. Additional windows are drawn for graphs.

If the viewer is run as an applet it can only be removed by leaving/destroying the html page that started the applet. The separate graphs can be removed using the [X] window tool on each window as required.

Figure 1 Main viewer showing the coordinate, sequence and palette panels

The Palette panel consists of buttons and drop down buttons. A drop down button is shown within a triangle to the right of the button. If a drop down button is picked then it remains dropped down until a second pick is made in the palette panel. It does NOT use a click and drag action. No action is performed on the palette or an open drop down if an area of the panel is clicked that is not a button. When a drop down button is open only the tools on the drop down are available and all other picks on the panel will close the drop down and result in no action.

Any button that is picked that results in some functionality will change the cursor to the system dependent wait cursor until the function selected has completed. The only exception is Surface/Calculate that submits a surface calculation and does not wait for completion.

Any button that controls a currently active function has red text with tick. Blue text is used for an inactive function or a button that does not have activity associated with it.

Figure 2: Part of the palette from the viewer with an open drop down for the surface function. Calculate is active indicating that surfaces have already been calculated, and the ligand surface is currently displayed and the protein surface is not displayed

The Structure view region uses functionally written by M. Hartshorn, AstexViewer™, Astex – although some additional features have been added. (Figure 3) The molecule is drawn as a bond-stick diagram, a ribbon or net surface. The view can be manipulated by a virtual track ball action (Left mouse button + drag of mouse); the molecule is rotated about y=0 and x=0 of the screen. The structure viewer is depth-cued and clipped to enhance the 3D effect, and perspective is not applied. The viewer can display objects by colour, text annotations and highlights as thick lines.

Figure 3 : the structure viewer with ligand surface included

An atom/residue/chain/molecule is selected from the view using a left mouse button click close to any atom. An atom is any vertex at the end of one or more drawn bonds. The selected atom and parent objects are indicated using the status line at the bottom of the viewer window. Any selection from this or other panels will result in the structure viewer updating its view focus. The view focus can either be as whole molecule (zoom out), or as a single residue and ~8A region about this residue. A selection using a mouse pick will either fly the molecule view or snap to the focus. A fly change has two modes. A change of focus to a region close by (less than 6A) will result in a translation to this new region. A large change of focus will result in the view flying out to "zoom out", then flying in to the new focus.

The structure viewer is designed to only load a maximum of 8 molecules at any one time. This is to prevent overload of both memory and CPU resources, as protein structure information is large. The loading and unloading of molecules is carried out using the sequence view panel. The left hand edge of the

Figure 4: The structure loading data

the sequence panel contains the sequence name and structure number (figure 4). Any sequence entry where the structure number is indicted using a "-" is not currently loaded into the structure viewer. The numerical value shown indicates the load order of the structures. Any sequence entry with no load number or "-" has no associated structure, and selecting this name will no affect. Picking the name of an already loaded structure will update the load order, so that the picked name will become the newest one with a numerical designation of "0". To load an unloaded structure into the structure viewer then the sequence file name (shown magenta in figure 4) is selected, a structure number will appear after the structure has been loaded. The structure with the oldest structure number (shown here as 12 for structure ten) will be unloaded from the viewer, and a "-" will replace the number.

The sequence panel displays sequence information as strings of letters on coloured boxes (figure 5). It is normal that the letters conform to the 1 letter code of the amino acid sequence, but the viewer will display any desired string of characters. The sequence viewer has no limit to the number of sequences that can be displayed, and all sequence within a single group will be displayed at any one time. Additionally, sequences not in any group will also be displayed. The left-hand region of the sequence panel shows the molecule/chain designation name and the structure load number (figure 4). The viewer will also render point information (such as active site residues) and join information (such as disulphide bonds). The viewer can highlight a single residue, and a column of selected residues, the former as a black background letter, and the latter as a black outlined boxes. The viewer has two different display modes, flat scrolled and hyperbolic. With the former, the sequence is shown as a string that scrolls left and right and out of the viewer edge. Any information outside the viewer edge cannot be seen. A hyperbolic view show the sequence distorted using a tanh function, so that the central portion of the sequence and annotation is at full resolution, while the peripheral regions are progressively compressed. This view has the advantage that the entire sequences + annotations can be viewed all the time.

Figure 5, the sequence shown using the hypobolic view and active site marks

The sequence view can be manipulated by a click and drag action (left mouse button), or using the scroll bars. A change of focus will place the selected residue at the centre of the display and highlighted it. A focus change can be carried out by selecting a residue from the structure viewer, sequence viewer or graph. Any change in the sequence focus will either snap to the new residue, or fly to the new residue by scrolling.

If a sequence entry is picked and this has an associated loaded structure, then the structure viewer and sequence viewer will update to this picked residue. If there is no associated structure then only the sequence viewer will update. If there is an associated structure, but it is not loaded within the structure viewer (as indicated by the load number "–" see figure 4), then a warning will be issued, and only the sequence viewer will update. Unloaded structures are loaded by selecting the sequence name at the left of the view for the unloaded structure.

A user can draw a graph containing data from the current visible molecule using the graph button drop down and this will appear in a separate window. This window will contain the requested graph, and can be closed using the [X] window remove button on the top border. The user cannot control the graph display type at the current time. The graph display supports highlights, colour and text annotations. Any selection from the sequence, structure or graph will highlight the residue selected using a solid circle, and add an annotation to the base of the graph indicating the molecule, chain and residue selected.

Figure 5. Ramachandran graph