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Menus in View Compound Workbench
Groups Menu
The Groups menu contains these menu items:
The Groups menu provides menu items for specifying selections of atoms as groups. When you have defined and named a group, you can display it in the 2D workspace as its alias. For further discussion, see To define and use groups.
Group
The Groups/Group menu item specifies that the selected set of atoms and bonds be known as a group of objects with a unique name. Select the atoms and bonds before selecting the menu item.
Selecting Groups/Group opens a control panel which prompts for the name and alias to be assigned the group. The group can be displayed as its alias in the 2D workspace by selecting the group (see Select Group) and then selecting the Groups/2D Group Style menu item and choosing the Symbolic option.
Ungroup
The Groups/Ungroup menu item ungroups a selected group. Select the Groups/Select Group menu item to select the group before using the Groups/Ungroup menu item.
Select Group
The Groups/Select Group menu item allows you to select a defined group of atoms.
To select a defined group of atoms, first select a single atom or bond that is a part of the group. Then select the Groups/Select Group menu item. Another menu appears, listing all the groups of which the selected item is a member. (If the selected item is not in any group, then the menu is empty.) Choose the group to be selected from the menu.
The group becomes selected, although you see no change in the workspace. The individual atoms and bonds in the group do not become highlighted, since the group has been selected as a whole, not the individual components.
After selecting a group, you can ungroup it, or you can display it symbolically in the 2D workspace.
Define R-Group
The Groups/Define R-Group menu item specifies that the selected set of atoms and bonds be known as a group with a unique name. Select the atoms and bonds before using the menu item.
This menu item automatically assigns a name and alias to the group. The name and alias are the same, and they take the form Rn, where n is an integer that increases by 1 each time you use Define R-Group for a new group. That is, the first group defined by this menu item receives the name and alias R1, the second is named R2, the third R3, and so on.
2D Group Style
The Groups/2D Group Style menu item allows you to display groups either as the collection of atoms and bonds that make up the group or as the group's alias. This menu item determines the display style for groups that you create and for groups that you add from the Periodic Table.
This menu item has two choices, Canonical and Symbolic:
Modeling Menu
The Modeling menu contains these menu items:
The Modeling menu allows you to choose the factors to be considered during dynamic modeling.
Dynamic Bond Rotations
The Modeling/Dynamic Bond Rotations menu item allows you to choose whether dynamic modeling occurs during rotation of a single bond. When you rotate a bond, you select a particular end of the bond, and then the part of the molecule connected to that end of the bond rotates as the bond rotates. If dynamic modeling does not occur during rotation, the unrotated part of the molecule remains unchanged. If dynamic modeling occurs, then atoms and bonds in the unrotated part of the molecule change their positions also, as necessary to maintain optimal bond lengths and angles. Other bonds in the molecule then respond to the torsion forces applied by rotation of the bond and to the forces selected from the Modeling menu. See To move atoms, rotate bonds, and flip topology for more information.
The Dynamic Bond Rotations menu item is a toggle. If the box next to the menu item is highlighted, then bond rotation invokes dynamic modeling. If the box is not highlighted, then the unrotated part of the molecule is unchanged by rotation.
van der Waals Forces
If the Modeling/van der Waals Forces menu item is selected, van der Waals forces are calculated and applied during dynamic modeling.
The van der Waals Forces menu item is a toggle. If the box next to the menu item is highlighted, then van der Waals forces are calculated during dynamic modeling. If the box is not highlighted, then van der Waals forces are not taken into consideration during dynamic modeling.
Tools Menu
The Tools menu contains these menu items:
The Tools menu provides tools for performing chemistry manipulations such as aromatizing, reducing, oxidizing, and protonating. Other Tools menu items improve the appearance of molecules in 2D and 3D and minimize them. The Tools menu also provides items for generating and evaluating conformers and for comparing conformers and hypotheses.
Chemistry/Aromatize
The Tools/Chemistry/Aromatize menu item makes atoms and bonds in a selected ring aromatic, if chemically possible. Otherwise it gives a warning. You must select at least one atom or bond in the ring to be aromatized before selecting this menu item.
To de-aromatize a ring, select the whole aromatic ring and then select the single-bond tool in the toolbox.
Chemistry/Oxidize
The Tools/Chemistry/Oxidize menu item increases the oxidation state (valence) of selected atoms by a maximum of two. Catalyst attaches an oxygen substituent (either =O or -OH) to the atom being oxidized. Charged atoms cannot be oxidized with this menu item.
To oxidize one or more atoms, select the atoms to be oxidized and then select the Tools/Chemistry/Oxidize menu item. The atom is oxidized, and the appropriate oxygen functionality is bonded to the molecule. For example, the sulfur atom in the example molecule below can be oxidized twice.
Chemistry/Reduce
The Tools/Chemistry/Reduce menu item decreases the oxidation state (valence) of the selected atoms by a maximum of two. Catalyst deletes a hydrogen or oxo (=O) from the atom being reduced. Charged atoms cannot be reduced with this menu item.
To reduce one or more atoms, select the atoms to be reduced and then select the Tools/Chemistry/Reduce menu item. The selected atom is reduced, and the appropriate oxygens or hydrogens are removed. In this example, the phosphorus and sulfur can be reduced simultaneously if they are both selected before selecting the Tools/Chemistry/Reduce menu item. Notice that the sulfone is reduced to sulfoxide, not sulfide:
Chemistry/Protonate
The Tools/Chemistry/Protonate menu item adds a bound proton to the selected atoms. To protonate, the selected atom must have a coordination number less than 4 and a net charge of zero or less. To deprotonate, region-select and delete a hydrogen on the target atom.
For example, for the Ala-Ala molecule below, select the primary amine's nitrogen and then the Tools/Chemistry/Protonate menu item. Region-select the hydrogen on the hydroxyl and delete it with the eraser tool. The zwitterionic form of the dipeptide is formed:
See To protonate an atom for more information.
Flip 2D
The Tools/Flip 2D menu item flips the images displayed in the 2D workspace horizontally or vertically. Select the Tools/Flip 2D menu item and then select ...About Vertical Axis or ...About Horizontal Axis from the submenu that appears.
2D Beautify
The Tools/2D Beautify menu item redisplays the selected molecule in the 2D workspace so that it is aligned from left to right, with correct bond angles and vertically aligned rings.
After selecting the 2D molecule to be beautified, select the Tools/2D Beautify menu item. For additional information, please see a molecule cleanup and alignment example.
Generate Standard 3D
The Tools/Generate Standard 3D menu item generates a typical 3D structure for the selected topology, which has correct bond lengths and angles, staggered chain geometry where possible, and no significant van der Waals overlaps. This action attempts to generate a structure that is easy to visualize, so it tends to produce extended structures that are not the lowest-energy structure.
After selecting the 3D molecule to be beautified, select the Tools/Generate Standard 3D menu item. For additional information, please see a molecule cleanup and alignment example.
3D Minimize
The Tools/3D Minimize menu item displays a 3D structure that corresponds to an energy minimum close to the current 3D structure of the molecule. This action finds a structure corresponding to a local energy minimum for the existing structure, which is not necessarily the structure with the lowest possible energy.
Compare/Fit
The Tools/Compare/Fit menu item performs a geometric comparison of pairs of compounds or hypotheses. The type of comparison performed depends on the types of objects selected:
- Two compounds -- Perform an rms geometric comparison of selected atoms in the two compounds, including Fast Fit or Best Fit on the conformers of one or both compounds.
- A compound and a hypothesis -- For a hypothesis with feature weights, check that geometric constraints are met and then perform a weighted geometric fit of matching features. For a hypothesis without feature weights, perform an rms geometric comparison of selected features in the two objects.
- Two hypotheses -- Perform an rms geometric comparison of matching features.
For additional information on Compare/Fit, please see What does the Compare/Fit action do?.
Orient 3D to 2D
The Tools/Orient 3D to 2D menu item rotates and aligns a selected molecule in the 3D workspace, without changing its configuration, so that it is oriented as closely as possible with its 2D structure.
After selecting the molecule to be reoriented in 3D, select the Tools/Orient 3D to 2D menu item. For additional information, please see a molecule cleanup and alignment example.
Show Conformational Model
The Tools/Show Conformational Model menu item opens a control panel that contains a 3D workspace to view and manipulate a set of conformers representing the conformational model for a compound. You can look at the conformers by stepping through them one at a time or by having Catalyst step through them automatically.
For more information, see To display, delete, register, and unregister individual conformers.
Generate Conformational Model
Use the Tools/Generate Conformational Model menu item to generate conformers for one or more molecules. Before you use this menu item, select from the workbench shelf those compounds for which you want to generate conformers. Selecting this menu item opens the Generate Conformational Model control panel. Names of selected compounds are displayed in the scrollable Compound List in the control panel. (If no compounds are selected, you'll see the word zero in the list box and you should click the Cancel button and begin again, selecting one or more compounds before selecting Tools/Generate Conformational Model.)
In the Generate Conformational Model control panel, fill in the boxes according to how you want the conformers to be generated:
- Maximum Number of Conformers to generate.
- Fast or Best Quality generation.
- Enter the Energy Range for the conformers.
- If you are generating conformers for more than one compound, the generation must be set up as a background process. If you want the job to run on a machine other than the one on which you are currently running Catalyst, select the Job Options button and fill in the Job Options control panel as described under To set up a conformer generation background process. (Conformers for a single compound can be generated within Catalyst or as a background process.)
When you have filled in the boxes, select the Generate button. This starts the generation of conformers if you chose Run within Catalyst or sets up the background process if you chose Run as Background Process. When the generation or setup is complete, the control panel disappears. When the conformer generation process runs, Catalyst generates conformers for each selected molecule in turn, using the parameters specified in the control panel for each one.
If the process runs within Catalyst, the conformers are automatically added to the compound. If the process runs in the background, you must use the Data/Process Information menu item in the Stockroom to check on the status of the operation and to retrieve the conformers when the generation process is finished. You also can use this menu item to cancel a running process. For more information on using the background process control functions, please see Process Information.
To see the conformers that were generated, use the Tools/Show Conformational Model menu item. For more details on how to generate conformers, please see To generate conformers.
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Last updated April 2000.
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