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Chapter 45. Gview
Gview is the application used by GRID to visualize Molecular Interaction Fields (MIF) and molecular structures. Molecules and MIF are represented as objects in an interactive 3D scenario where the User can rotate, translate and scale these objects. The application can also be used to export the data to standard formats (Sybyl, InsightII) and to print the images.
The Gview is a stand-alone application usually started by command line:
gview filename
where filename is a GRID Molecular Interaction Field (kont file). If the GRID installation directory is not set in the PATH environment variable, the command should be preceded by the full path (i.e. /usr/local/GRID/gview filename).
Gview can also be used to display (macro)molecule structures by typing:
gview filename
where filename is a molecule structure in one of the supported molecular formats.
45.1. Graphical representation of MIF
In the simplest case, a GRID kont file might contains the MIF describing the interaction of a single molecule with a single probe. However, sometimes the kont contains the MIF of several structures and probes (see Studying a Set of Structures). In these cases, gview will show only a single MIF at a time, which can be chosen from a list of all the MIF's included in the kont of changed pressing the <Up> and <Down> arrow keys for changing the structure and the <Right> and <Left> arrow keys for changing the probe.
In Gview, every MIF can be represented by one or many isovolumes, which enclose the regions of the space for which the values of the MIF are higher than a certain defined threshold (for positive values) or lower than a certain defined threshold (for negative values).
Sometimes it is interesting to display simultaneously more than one MIF obtained from the same GRID kont, for example, to display isovolumes representing hydrophobic and hydrophilic regions around a molecule simultaneously. The only way to do this in Gview is to load the same GRID kont twice and to select a different MIF (probe 1 and probe 2 for the same molecule) for both instances.
When importing kont files obtained for set of structure, Gview will try to load also the molecular structures associated with the MIFs. Alternatively, molecular structures can be imported into the 3Dplot, either using the drag an drop import mechanism described below, or the command File->Open...
45.2. Drag and drop import
The simplest and fastest way to import molecules or field fields into Gview is to use "drag and drop". For using this mechanism, start by opening the folder containing the structures using a graphical file manager (i.e the Indigo Magic Desktop in SGI platforms, Nautilus in Gnome Linux or Konqueror in KDE Linux). Open the file manager and navigate through the directory tree until you see the files that you want to import. Select one or more icons and drag and drop them on the Gview 3Dplot. Gview will read the file(s) and import them one after the other.
By default Gview will colour the first imported structure "by atom type" and will assign different palette colours to successive structures, if any.
Gview recognizes the format of the molecular structure by the extension of the file. If you try to import a file with a wrong extension or without any extension, the import can fail. The following extensions are recognized:
45.3. Mouse interaction
In Gview the mouse has different uses depending the application mode:
| mode | key | cursor | uses |
| pick | <T> toggles between pick-browse | arrow head | Click on any atom with the left mouse button to highlight the atom and show a label (named click label) identifying the molecule name, the atom name and the residue name (for PDB files). The aspect and color of the click labels can be customised in the Edit>>>Preferences dialog |
| measure | Hold SHIFT key pressed in pick mode | arrow head | Click on two atoms or nodes displays the distance in Angstroms. Click on three atoms or nodes displays the angle in sexagesimal degrees. Click on four atoms or nodes displays the dihedral angle in sexagesimal degrees Distances and angles are displayed persistently in the 3Dplot and temporarily in the status bar |
| browse | <T> toggles between pick-browse | circle | Move the mouse with the left button depressed to rotate the molecules and the data. Move the mouse with the central button depressed to translate the molecules and the data Move the mouse with both the left and central buttons depressed from top to bottom to change the scale |
In pick mode, it is possible to press <SHIFT-Alt> to change to browse mode temporarily, and the pick mode will be restored when the key is released. This allows to rotate or translate the molecule without actually exiting from the pick mode.
45.4. Gview status line
From version 2.0, Gview contains a status line showing permanent information about the molecules and MIF loaded as well as temporary messages. The status line looks like this:
From left to right there can be distinguished three different sections:
| messages | shows temporary messages, like the success of loading and saving files, the changes on the cursor status and the values of the measurements (distances, angles and dihedrals). Messages printed in this section will last only for five seconds |
| molecules | This region shows the name of active molecule, and its order in the total number of molecules. In the figure, there is only one molecule loaded and its name is "diazepam".The active molecule is the last loaded molecule or the last in the list of the selected molecules, when the selection dialog is active.Messages printed in this section are persistent. |
| fields | This region shows first the name of active data and its order in the total number of data files, and its order in the total number of molecules. In the figure, there is only one data file loaded and its name is "diazepam".Next, it is shown the name of the active MIF which is identified by the name and ordinal number of the molecule and the the ordinal number of the probe. In the above figure the data contains only the MIF for a single molecule and two probes and the active MIF is the one corresponding to the fist probe.Messages printed in this section are persistent. |
45.5. Gview menu
FIXME: In this reference section etc....
45.5.1. File (Alt-F)
45.5.1.1. File->Open... (Ctrl-O)
Opens a standard dialog where the User can select the file to import for visualisation.
By default, only the files with extensions mol2, pdb, ent, car, cor and kout (molecules) are shown. Change the File type to show files of type Field (extensions .kont) or Any file.
Select the file from the list and press the Open button to import the file or press the Cancel button to exit.
The file can contain molecules or MIF. Gview will recognize the file type using the standard extensions and deal automatically with the different file formats. The following extensions are recognized:
| .mol2 | TRIPOS Sybyl mol2 |
| .car .cor | BIOSYM InsightII car |
| .pdb .ent | Protein Data Bank, as defined in version 2.0. Connectivity section is not needed nor used. |
| .kout | GRID kout |
If you try to import a file with a wrong extension or without any extension, the import will fail.
The first molecule imported will be colored by atom type. Successive molecules will be colored of different palette colors.
45.5.1.2. File->Save...
This command is accessible only when some MIF have been loaded.
Gview can save the Molecular Interaction Fields in InsightII (.grd) or Sybyl (.cnt) formats. The command opens a standard dialog where the User can set the name of the output file.
By default, only the files with extensions grd (InsightII grid) are shown. Change the File type to show files of type Sybyl (extensions .cnt).
Select a file name from the list or type a new file name and press the Save button to import the file or press the Cancel button to exit. If the export is successful, a message will be show in the application status bar.
Please refer to the respective manual of these applications for details about how to import.
45.5.1.3. File->Print... (Ctrl-P)
Gview can send the contents of the screen directly to a printer. The User can define output options in a standard dialog like this.
Select the appropriate options and then press the OK button to print the 3Dplot contents or press Cancel to exit.
45.5.1.4. File->Exit (Ctrl-X)
Use this command to exit from the application.
45.5.2. Edit (Alt-E)
45.5.2.1. Menu Edit->Molecule style... (Ctrl-M)
This command is accessible only when some MIF have been loaded.
The command opens a dialog with two tabs. The first tab (Molecule) describe settings of single bond and atom rendering. The second tab (Biopolymers) describes the format of schematic representations which are available only for biomolecules like proteins and nucleic acids.
Selections made using this command directly from the menu will be applied to every molecule present in the 3Dplot. If you want to select the rendering style of only one molecule, please select the molecules using the Edit>>>Select command before.
45.5.2.1.1. Molecule tab
- Rendering-style
Atoms and bonds can be rendered in one of the following styles: wireframe, sticks, ball&sticks and CPK. Wireframe is fast and usually a good choice for large molecules. Sticks and balls&sticks is preferable for small molecules. CPK representation allows one to appreciate the volume of the molecules. It is also possible to avoid the representation of atoms and bonds by selecting the option hide atoms.
- Rendering-hydrogen
The hydrogen atoms can be shown or hidden.
- Rendering-quality
The quality of the rendering can be selected in a range between 0% and 100%. Better qualities look nicer in the screen but are also more computationaly demanding and can slow down considerably the rendering and the movement of the molecules. Defaults are generally a good compromise for most hardware platforms but can be increased for generating publication-quality pictures or decreased for representing large molecules or in less-powerful computers.
- Size-wireframe
Thickness of the lines used in wireframe rendering style.
- Size-sticks
Thickness of the sticks used to represent bonds in both the sticks and balls&sticks rendering styles.
- Size-balls
Size of the balls used to represent atoms in balls&sticks rendering style.
- Color-from property
By selecting this option, the atoms will be coloured according to one of the following schemes:
atom type Atoms are colouring according to an standard colouring scheme: carbon is grey, oxygen red, nitrogen blue, etc... property This option is applicable only to PDB files. In these, the atoms will be coloured according to the value present in the Thermal factor field (columns 61-66) using a spectrum from red to blue. - Color-from palette
By selecting this option, the atoms will be uniformly coloured. The actual colour can be chosen clicking in the ... button. This will pop-up a standard colour selection dialog like this.
- Atom labels
Every atom can be labelled using a short string of text describing the atom type (chemical element), atom name (label inserted into the original file) and atom number (as indicated in the original file). Selecting no labels will disable the representation of atom labels. The colour used for the label can also be chosen clicking in the .. button. This will pop-up a standard colour selection dialog like this one.
45.5.2.1.2. Biopolymers tab
- Rendering-style
Residues can be rendered in one of the following styles: backbone wire, backbone tube line ribbon, flat ribbon, solid ribbon and cartoons. None of these representations is computationally demanding. Backbone representations link the alpha carbon in proteins and the C3' in DNA, ribbon and cartoon representations pass near these positions and are particularly well suited when the original file includes a explicit definition of the secondary structural elements. It is also possible to avoid the representation of residues by selecting the option hide bio.
- Rendering-quality
The quality of the rendering can be selected in a range between 0 and 100. Better qualities look nicer in the screen but are also more computationaly demanding and can slow down the rendering and the movement of the molecules. Defaults are generally a good compromise for most hardware platforms but can be increased for generating publication-quality pictures or decreased for representing large molecules or in less-powerful computers.
- Size-lines
Thickness of the lines used in backbone wire and line ribbon rendering style.
- Size-tube
Thickness of the tubes used in backbone tube rendering styles.
- Color from property
By selecting this option, the biopolymer representation will be coloured according to one of the following schemes
- Color from palette
By selecting this option, the biopolymer representation will be uniformly coloured. The actual colour can be chosen clicking in the ... button. This will pop-up a standard colour selection dialog like this one:
- Residue labels
Every residue can be labelled using a short string of text describing the residue name (in 1 letter or 3 letter format) and number. Selecting no labels will disable the representation of residue labels. The colour used for the label can also be chosen clicking in the ... button. This will pop-up a standard colour selection dialog like this.
The changes are immediately applied to the molecule/s of the 3Dplot. To close this dialog press the Exit button.
45.5.2.2. Edit->Field style... (Ctrl-F)
Molecular Interaction fields admit no direct representation. One of the most popular ways to represent the information contained in a MIF is the rendering of isovolumes. An isovolume is a region of the space which encloses values of the MIF within a certain range, typically, values higher that a cutt-off (when the cut-off is positive) or lower than a cutoff (when the cutt-off is negative).
This command allow the user to create, edit and remove isovolumes for any of the currently displayed MIF. Any number of isovolumes can be inserted in the 3Dplot and every one can be edited separately.
The dialog contains two tabs, one for defining the most usual options (isovolume edition, threshold change and rendering style) and a second tab for setting the details of the rendering (symbol type and size, contour planes, special colouring schemes and box extents rendering).
45.5.2.2.1. Field tab
- isovolumes list
The window represent a hierarchical tree which shows for every GRID kont file loaded, the list of isovolumes currently defined. For every isovolume it is shown:
a small check box which can be used to show or hide temporarily the volume
the rendering style (solid, contour or symbol) and colour (as the label background)
the threshold level
the transparence percentage
The buttons on the right hand side of the window can be used to add new isovolumes to the list or to delete the currently selected isovolume.
For editing the rendering settings of a isovolume, the first step is to select it in this list. All the settings apply only to this currently selected isovolume.
- Energy Level
The scale defines the cutoff value applied to the currently selected isovolume:
For positive values, the surface or contour will enclose all the field nodes with values higher than the positive cutoff.
For negative values, the surface or contour will enclose all the field nodes with values lower (more negative) than the negative cutoff.
The cutoff can be adjusted by moving the slide or by entering the actual value in the numeric field on the right hand side. Please notice that when solid surfaces or contour styles are selected, the graphic changes interactively but in the case of symbols, the graphic is updated only when the User releases the mouse from the scale.
Allowed values range from the minimum to the maximum values found in the current MIF. If the current MIF is changed while this dialog is open (for example, pressing the arrow keys), the values can be adjusted according with the maximum and minimums of the new current MIF.
- Rendering-style
Allows the User to change the representation style of the data between solid surfaces, contours and symbols or to hide it. Surface and contours use solid surfaces or lines delimiting the extents of the isovolumes. In the symbols representation mode, each grid node within the range defined by the positive and negative cutoff will be represented by a symbol (a cross, a cube or a sphere) of a size proportional to the absolute value represented. For example: a sphere representing a value of 0.03 will be bigger than a sphere representing a value of 0.02.
- Rendering-colour
Allows the User to change the colour used to represent the currently selected isovolume. Pressing the ... button will pop-up a standard colour selection dialog like the following:
- Rendering-transp
Moving this slider, the User can select the transparency level of the solid surfaces for the currently selected isovolume. Symbol and contour representations are not affected by this setting. The User should be warned that the rendering of transparent surfaces can be very computationaly demanding in some computers, particularly those without hardware-accelerated graphics.
45.5.2.2.2. Style tab
- Symbols-type
Define the type of symbol to use: crosses, spheres or cubes. The faster representation is obtained with crosses, but spheres and cubes can produce nice and clean representations in some cases. As a general rule, do not try to use symbol representations for very large fields (more than 100.000 grid nodes) because the rendering of the plot can be very slow. In these cases use surfaces or contours.
- Symbols-size
Define the base size used for the symbols, in arbitrary units.
- Contour planes
In isocontour representations, these controls toggle on and off the display of the contour lines in the X, Y and Z planes.
- Field colouring scheme
By default, the isovolumes are given a consistent (flat) colour. However, if the current MIF has been generated using the GRID ALMD directive set to a value higher than 0.00, the MIF contains information about the atoms making the more significant contribution to every MIF node. This information can be used to colour the isovolume nodes, either by the colour of the corresponding atom type (provided that the molecule structure is also present in the 3Dplot) or by randomly selected high-contrast colours.
This is a rarely used set, but very useful for identifying the atoms responsible of a certain MIF value. More explanations can be found in ALMD directive.
- Field box
Toggles on and off the display of a cube representing the extents of the grid cage. The colour of the lines could be either white or black depending on the background colour.
The changes are immediately applied to any at the time rendered MIF; to close this dialog press the Exit button.
45.5.2.3. Edit->Select... (Ctrl-S)
This command opens a dialog with two tabs. In the first tab, the User can show/hide individual molecule structure(s) and also select them for editing the rendering style and deleting from the 3Dplot. In the second tab the User can select a certain MIF for editing its rendering style and deleting from the 3Dplot. If the MIF imported contains data for several probes and/or molecules, it is also possible select from this menu the single combination of molecule and probe represented in the 3Dplot.
45.5.2.3.1. Molecule tab
Every molecule inserted in the 3Dplot is listed in the window, identified by a molecule name corresponding to the file name from which it was imported without the extension. The list contains a small check-box which can be used to show or hide temporarily a certain molecule. In this tab it is possible to select more than one molecule at the same time. Selected molecules are highlighted in the 3Dplot by enclosing the atoms in small yellow boxes.
- clear sel
This button deselects any molecule, both from the dialog and from the 3Dplot
- invert sel
Pressing this button makes that the selected molecules became unselected and viceversa
- edit sel
This button deselects open a Molecular style dialog identical to the one described above but in this case the changes will be applied only to the molecule(s) selected.
- delete
Removes the selected molecule from the list and from the 3Dplot
45.5.2.3.2. Field tab
The window shows a hierarchical lists with the GRID kont file loaded and for every field, the names of the different MIF identified by the name of the molecule and a sequential number corresponding to the probe used for the analysis.
In this list it is possible to select only one item at a time. The selected MIF becomes then the current MIF for the corresponding GRID kont.
Sometimes it is interesting to display simultaneously more than one MIF obtained from the same GRID kont, for example, to display isovolumes representing hydrophobic and hydrophilic regions around a molecule simultaneously. The only way to do this in Gview is to load the same GRID kont twice and to select a different MIF (probe 1 and probe 2 for the same molecule) for both instances.
- edit style
Shows a Field style dialog allowing to edit the style settings for the current MIF
- delete
Removes from the list and from the 3Dplot the selected GRID kont and every associated MIF and isovolume. For removing individual isovolumes, please use the Edit>>>Field style... command.
45.5.2.4. Edit->Clean labels
This command will remove from the 3Dplot all the click labels. These labels are shown as a response of a click on any atom or grid node and should not be confused with the atom and residue labels which can be added in the Edit>>Molecule style dialog
45.5.2.5. Edit->Clean measures
This command will remove from the 3Dplot all the measurements.
45.5.2.6. Edit->Clean gadgets
This command will remove from the 3Dplot specific gadget elements like manipulator boxes, symbols, etc... which can be introduced by other programs like Greater for specific pourposes.
45.5.2.7. Edit->Preferences...
Opens a dialog where the User can select some preferences of the application. These preferences are persistent and different for every user.
The dialog contains four tabs
45.5.2.7.1. 3D scenario tab
- Rendering preferences
fog enable/disable fog. When enabled, some fog is added to simulate the depth and objects far from the observer will appear darker. spin enable/disable spin animation. stereo enable/disable dichroic stereo. When enabled, the User can see the images in stereo using inexpensive red and blue filter glasses. perspective enable/disable perspective. When perspective is on, objects far from the observer look smaller, when it is off an orthographic perspective is used. Perspective on is useful for small molecules, but can make it difficult to visualize large molecules. - Background
Shows a dialog where the User can select the background colour. Clicking the ... button will show an standard colour selection dialog from which the User can select the colour. The same colour of the background is applied to the fog, when it has been enabled.
45.5.2.7.2. Click labels tab
- Label format
When the mouse picking mode is active, the atoms selected are labeled using a string which might containing different information, according to the check boxes selected.
The name of the atom. One or two characters in uppercase plus the sequential atom number.
The name of the residue: three characters identifying the type of the residue and other three identifying their number.
The name of the molecule.
Please notice that if you leave all checkboxes unselected, clicking on any atom in pick mode will produce no visible label.
- Label aspect
If the click labels are persistent, a different label will be added every time the User clicks on any atom. When non-persistent labels are chosen, the last click label added will be removed before adding a new one.
The colour and font size will define the aspect of the click labels. Pressing the ... button will show an standard colour selection dialog from which the User can select the colour of the labels.
45.5.2.7.3. Fonts tab
This tab defines the fonts used for permanent labels, the ones used to label atoms or residues as defined in the Edit>>>Molecule style...dialog. Not all fonts produce a good rendering in the 3Dplot.
45.5.2.7.4. Advanced tab
In this tab, the User can select the overall rendering quality of the 3Dplot. The default setting (Adaptative render), is the best choice in most cases, but it can be changed to improve the performance and/or the rendering quality in certain configurations. In particular, if Gview is used in remote mode, exporting the display to a local X terminal or emulator, the best results are obtained using the compatibility models (either GLU or OpenInventor). If the changes are applied while the scenario contains molecules rendered in CPK or balls&sticks mode, the 3Dplot can flicker repeatedly while the redrawing is completed.
The antialias check box defines if the lines used in the 3Dplot use or not smoothing algorithms to reduce the "scale" effect. The impact of this setting in the aspect and in the performance can be remarkable and is rather different depending on the hardware platform.
Changes are applied to the scenario immediately. To exit from the dialog press Exit.
45.5.3. View (Alt-V)
45.5.3.1. View->Home (Ctrl-H)
Restores the original point of view and scale which were initially used when the application was first opened.
45.5.3.2. View->Full view
Applies a camera position and scale which allows the entire content of the scenario to be visualised.
45.5.3.3. View->Copy view (Ctrl-C)
The position of the virtual camera and the scale is stored in an internal clipboard, common for all applications in the Desktop. Select View>>Paste view in the same or in a different Gview application to restore this point of view.
This option is very useful to show exactly the same point of view in different Gview applications representing different data.
The view can be copied and pasted only between applications using the same type of cameras. If one of the Gview cameras is using perspective and the other is not, the copy and paste will not work.
45.5.3.4. View->Paste view (Ctrl-V)
The position of the virtual camera and the scale, stored in the internal clipboard using View>>>Copy view, are applied to the current scenario.
This option is very useful to show exactly the same point of view in different Gview applications representing different data.
The view can be copied and pasted only between applications using the same type of cameras. If one of the Gview is using perspective and the other no, the copy and paste will not work.
45.5.3.5. View->Toggle mode (T)
Toggle this control to change between view mode and pick mode. The different mouse modes were described above.
45.5.4. Help (Alt-H)
45.5.4.1. Help->Help... (F1)
This command opens a very simple HTML browser which can be used to consult on-line this manual. Some Help buttons in the application are linked to specific positions of the manual allowing an easy access to the corresponding chapters.
The Home, Back and Next button allow an easy navigation by the manual. Pressing the Print button it is possible to print the manual contents.
Press the Exit button to close this dialog window.
45.5.4.2. Help->About... (SHIFT-F1)
This command shows information about the version of Gview plus some credits.
45.5.5. Contextual Menu (Right mouse click)
The contextual provides an easy access to commonly used commands. It is shown when the user press the right mouse button. In order to use it, press the right mouse button and while keeping it pressed drag the mouse until the command is highlighted, then release the button.
The commands called by this menu are described in the corresponding sections.
45.5.6. Third party software
Gview uses OpenMOIV. OpenMOIV is an independent development of the Department of Technology, at the Universitat Pompeu Fabra, Barcelona (Spain). This library is distributed under the under GNU Lesser General Public License 2.1:
This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. |
Please visit the official home page of OpenMOIV for further information and the download of the library source code.
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