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Build Panel |
The Build panel is used to create structures by assembling them from fragments. A wide variety of fragments is provided. The panel also contains controls for changing atom and residue properties.
To open the Build panel, you can:
Choose Edit → Build → Fragments in the main window.
Choose Edit → Build → Atom Properties in the main window.
Choose Edit → Build → Residue Properties in the main window.
Click the Fragments... button on the Fragments toolbar in the main window.
The Build panel, combined with the Build and Fragments toolbars, provides tools for creating structures in the Workspace. You can build from fragments in Place mode or Grow mode, you can draw structures free-hand, and you can change residues in an existing structure in Mutate mode.
Structures that are built in Place mode or Grow mode are automatically added as project entries, with the default title StructureN, which you can change by editing the title cell in the Project Table or Entry List. Sturctures that are build in Draw mode are scratch entries, and you must create a project entry to save them. To create an entry, you can:
Choose Workspace → Create Project Entry in the main window.
Press Ctrl+Shift+N (⇧⌘N) in the main window.
Click the Create Entry button on the Workspace toolbar in the main window.
Right-click in the Workspace and choose Create Project Entry.
Select Place in the Fragments tab, select a fragment library from the Fragments menu, select a fragment, then click in the Workspace to place the fragment. To add a fragment to this structure, select a fragment, then click on the atom you want to replace with the fragment. You can also select fragments from the Fragments toolbar.
Select Grow in the Fragments tab, select a fragment library from the Fragments menu, then select a fragment. The fragment is automatically placed in the Workspace with a green arrow indicating the location where the next fragment is to be added (the grow bond). To add a fragment to this structure, select a fragment. To change the grow bond, choose Atom or Bond from the Define grow bond pick option menu, then select 2 atoms or 1 bond in the Workspace to define the bond. The grow direction is defined by the second atom selected or the half-bond selected.
When growing from a part of the structure that has a residue name, the new fragment inherits the chain name and a residue number is assigned. If the fragment that is grown has a residue name, its residue number is assigned by incrementing or decrementing the number of the residue number it was grown from; if it does not have a residue name, it is assigned the same residue number.
To create a new structure by free-hand drawing, click the Draw structures button (pencil) on the Build toolbar in the main window, choose an element from the button menu, then click in the Workspace to place atoms. The atoms are connected by single bonds. The atom enclosed in the purple cube is the active atom, to which the next atom will be joined. To finish drawing, click on the active atom. The active atom then becomes inactive. To select a new active atom, click on the active atom to deactivate it, then click on the desired active atom. To create a bond from the active atom to an existing atom, click on the existing atom. This atom becomes the new active atom. If the existing atom is already bonded to the active atom, the bond order is increased by one.
Once you have drawn a structure, you can move the atoms using the Move button on the Build toolbar. Choose a direction from the button menu and click on an atom to move it. Moves in the Z direction take place automatically in 0.5 Å increments. To move an atom in the XY plane, click the new location after selecting the atom to move.
If you draw a bond between molecules that are in different entries, this operation is considered to be a Connect operation. A single entry is created from the two source entries. If the entries are project entries, a new entry is created, which you can name. If one entry is a project entry and the other is a scratch entry, the scratch entry is merged into the project entry. If both entries are scratch entries, one scratch entry is merged into the other. See the Connect & Fuse panel for more information.
You can also draw structures in 2D, and convert them to 3D, in the 2D Sketcher.
To mutate residues in an existing structure, choose Amino acids from the Fragments menu in the Fragments tab. The Mutate option appears at the top of the tab. Select this option, select an amino acid from the fragments list, then click on the residue you want to mutate.
The Build panel contains three tabs. The Fragments tab contains a range of fragment types for building organic, inorganic, and biological molecules. The Atom Properties tab and the Residue Properties tab contain tools for changing atom and residue properties.
The Fragments tab provides tools for assembling structures from predefined fragments. There are two ways to assemble a molecule using fragments: Place mode and Grow mode. These modes are described below.
The Fragments tab features are:
These features are described below.
In Place mode, you can select a fragment from the fragments section of the tab and click in the Workspace to place the fragment. To join a fragment to the structure in the Workspace, select a fragment and click on an atom in the structure. The primary atom in the fragment replaces the atom on which you click. For example, the result of selecting methane, clicking once in the Workspace to place the first fragment then clicking on a hydrogen atom in this fragment is an ethane molecule. As a second example, if you place cyclohexane, select amine, and click on one of the carbon atoms in the ring, the result is piperidine. Attaching fragments usually results in reasonable geometries, but you might have to adjust the orientation. In Place mode, the Grow direction and Joining geometry options are ignored.
In Grow mode, fragments are "grown" onto the existing structure by replacing the atom (and any attachments) at the head of the grow bond. The grow bond is indicated by a green arrow. Attachment of new fragments always takes place in the direction of this green arrow. When you select a fragment in the fragments section of the tab, it is automatically grown onto the structure, and the grow bond is updated to a predefined location on the fragment just grown. The geometry in which the fragment is joined can be controlled from the Joining geometry option menu.
If a grow bond is not defined, Maestro searches for a suitable grow bond. If it cannot locate one, you must define one with the Define grow bond picking tools. You can also define your own grow bond with these tools. If you pick two atoms, the grow bond points to the second. If you pick a bond, the grow bond points to the atom nearest to where you clicked. Grow bonds cannot be bonds that are part of a ring. You can also reverse the direction of growth from the Grow direction option menu. If you reverse the direction, Maestro defines a new grow bond at the opposite end of the molecule.
When growing a new structure, it is not necessary to first place a fragment. The first fragment selected from the fragments section is placed in the Workspace.
When you select Amino acids from the Fragments menu, a Mutate option is added to the tools at the top of the tab. To mutate residues, select this option, click on an amino acid in the fragments list, then click on the residue in the Workspace that you want to mutate. The residue from the list replaces the residue in the structure.
The Fragments option menu provides access to various fragment libraries. When you choose a library from the menu, the members of the library are displayed in the pane in the center of the panel. The available libraries are:
These libraries are described below.
This library contains the common organic functional groups, a selection of simple ring structures, some common ions such as hydroxide, sulfate, nitrate, ammonium, and a hydrogen molecule.
This library contains more complex ring structures than those in the organic fragments library, including fused ring structures, a basic steroid structure, porphyrin and phthalocyanine, buckminsterfullerene, and dodecaborane.
The four heterocycle fragment libraries provide a range of ring structures that contain nitrogen, oxygen, and sulfur atoms.
Sugars can assume cyclized forms that include either five or six members. The five-membered ring form is called the furanose form and the six-membered version is called the pyranose form. The natural state of most sugars is the pyranose form, but some derivatives assume a furanose form. Maestro provides both options in both d and l forms.
These libraries contain common ligands used in inorganic chemistry and metal centers with various coordination numbers, but with the specific metal undefined. To change the metal type, place the molecule in the Workspace, click on the Atom Properties tab, choose using the Elements from the Properties option menu, select a metal and click on the metal atom in the Workspace.
The Amino acids library contains the 22 naturally-occurring amino acids. The Nonstandard amino acids library includes the D forms of the 22 amino acids and various other residues, such as hydroxyproline and phosphorylated serine and tyrosine. The Modified amino acids library includes the five residues MSE (selenomethionine), ASQ (phosphoaspartate), TPO (phosphothreonine), PTR (phosphotyrosine), and SEP (phosphoserine). The Protein capping groups library contains common molecules used to cap peptides. The Deoxyribonucleic acids library contains Adenosine, Cytosine, Guanine, and Thymine, while the Ribonucleic acids library contains Adenosine, Cytosine, Guanine, and Uracil.
This library contains common solvents and solvent ions found in protein structures, and is primarily intended for manual placement of these species in PrimeX. These fragments cannot be used for growing because they do not have designated grow bonds.
This is a collection of chemically diverse fragments with chains of various lengths attached to the main functional group. It is useful for examining SAR relationships. It is intended for use with MCPRO+ for free-energy perturbation calculations of relative ligand binding energies.
The option menus in the lower section of the panel change, depending on which fragment library is selected:
Grow Direction—displayed for all libraries. Selecting backward moves the grow bond to the opposite end of the molecule. For amino acids, forward is defined as N-to-C and backward as C-to-N
Joining Geometry—displayed for all except the carbohydrate and nucleic acid libraries. For amino acids and capping groups, you can choose between cis and trans joining geometries; for all other fragments the options are anti, gauche+, gauche-, and eclipsed or default.
Secondary Structure—displayed for the carbohydrate, amino acid, and capping group libraries. From this menu you can choose various helix and sheet arrangements, as well as extended structures.
Helix Geometry—displayed for the nucleic acid libraries. This menu allows you to choose the standard helix, or to define your own.
Fragment Type—displayed for the carbohydrate libraries, and provides alpha and beta options.
Duplex Conformation—displayed for the double-stranded DNA libraries, and provides options based on the helix formation chosen.
The tools in the Atom Properties tab allow you to change properties of the atoms in the Workspace. To see the values of the properties in the Workspace, you must include the properties in the atom label and label the atoms. The Properties menu lists specific properties that can be changed, and provides a general editing mechanism for any atom property. Each choice displays a set of tools in the lower part of the tab. The choices are:
When you choose Element from the Properties menu, a periodic table is displayed. To change an atom in the Workspace to that of another element, select Set Element, click the element in the periodic table, then click the atom in the Workspace. You can also change the element to a limited selection of elements using the Set Element toolbar button.
MacroModel atom type symbols describe the bonding, hydrogen atom and lone electron pair configuration around an atom. Each type of atom is appropriate only for certain force fields. When you choose Atom Type (MacroModel) from the Properties menu, a list of MacroModel atom types with their descriptions is displayed. To retype an atom, select Set atom type (MacroModel), select an atom type from the list, then click the atom to be retyped. The atom types are listed in Appendix C of the MacroModel Reference Manual and Appendix B of the Maestro User Manual.
When you choose Partial charge from the Properties menu, you can set both the partial charge and the solvation charge. The partial atomic charge is used in the electrostatic part of molecular mechanics calculations, and the solvation charge is used by MacroModel in GB/SA solvation calculations. In most circumstances, these should be the same value. To set the charges, enter values in the text boxes, then use the picking tools to select the atoms whose charge is to be set.
When you choose PDB Atom Name from the Properties menu, you can use the tools that are displayed to set PDB atom names and assign unique PDB atom names within residues. Only the first four characters of the atom name are used when you set the name. To set the name, enter a name in the PDB atom name text box, then use the picking tools to select the atoms to name.
According to the PDB standard, the first two characters should contain the element symbol, right-justified; the third character is a remoteness indicator (A=alpha, B=beta, G=gamma, etc.), and the fourth is a numeric branch designator, if applicable. So, a generic carbon atom should be _C__ with the _ characters indicating spaces. A peptide alpha carbon should be _CA_, and not CA__ which is interpreted as a calcium atom.
To apply unique PDB atom names within selected residues, use the Set unique PDB atom names within residues picking tools to select the residues to rename. The unique names are composed of the element symbol, right justified in the first two characters, followed by a numeric index for that element. The names are only unique within each residue.
Grow names are used when defining new fragments for the builder. Only the first four characters of the grow name are used. To set the grow name, enter the name in the Grow name text box and use the picking tools to select the atom for the grow name.
When you choose Atom Name from the Properties menu, you can use the tools that are displayed to set atom names, to define and assign canonical names, and to assign unique atom names. To apply a specific name to selected atoms, enter the name in the Atom name text box, then use the picking tools to select the atoms to which you want to apply the name. Because the "~" character is used to make unique names, this character cannot be specified in user-assigned names. To assign canonical names, choose a composition from the Composition menu, enter a separator of up to 4 characters in the Separator text box (if you want to change it from the default of a space), then click Apply To All Atoms. To make existing names unique, click Make Unique. If an atom has no name, the default canonical name consisting of element and atom number is used; if two or more atoms have the same name, a numeric suffix followed by a tilde '~' character is used to distinguish them from each other.
The Isotope number tools allow you to set the isotope number (mass number) for one or more atoms. You can specify the isotope in the text box, then apply it to atoms with the picking tools. The isotope number is used in calculations of molecular weight.
The isotope can be displayed in an atom label in two ways. If you choose the Isotope number property to include in the atom label, it is displayed as atom-isotope, e.g. C-13. If you choose the mass number property, only the mass number is displayed. For hydrogen, you can set a preference to display the element label as H, D, or T, depending on the isotope number, under Atom Labels in the Preferences panel.
When you choose Other, the tools that are displayed allow you to change the properties for any of the properties that do not have special editing tools. To edit one or more properties, select them in the Properties list. These properties are added as columns to the Atoms table. Next, use the Add atoms to edit their properties picking tools to select the atoms that you want to edit. The atoms are listed in the Atoms table by atom number, and the property columns are populated with the values. To change a property for an atom, you can edit the table cell. To set the value for multiple atoms, select the atom rows in the table, edit one of the table cells, and press Ctrl+ENTER (⌘ENTER) to apply the change to the selected rows. Selecting atoms in the table also selects them in the Workspace.
If you want to delete property values for all atoms in the Workspace, choose the properties from the Property list and click Delete. The property values are removed from all atoms in the Workspace (not just those in the table), and the property is removed from the Atoms table.
If you want to add a property to the atoms that are selected in the Atoms table, click Add. The Add Property dialog box opens, in which you can select the type, name the property, and provide an initial value. The property is added as a column to the Property table, and the values are added to the selected atoms.
The tools in the Residue Properties tab allow you to change properties of the residues in the Workspace. The properties that can be changed are available from the Property option menu. Each property choice displays a set of tools in the lower part of the tab. The available properties are:
When you choose Residue Number from the Properties menu, you can use the tools that are displayed to set the residue number for selected residues, and renumber residues within a structure.
To set the residue number, enter the number in the Residue number text box, and select the residue to apply the number to, or click the common objects button and choose Select to open the Atom Selection dialog box and define the residues whose number is to be set. If the residue number is incorrect for one or more atoms, you can pick atoms rather than residues to apply the residue number to.
To renumber residues, by incrementing the residue number, enter a starting number in the Renumber from text box, choose a structural unit from the Pick menu and select the units to renumber, or use the common objects button to select predefined atom sets or atom selections, or open the Atom Selection dialog box to define the residues to renumber. The residue with the lowest number in the selection is assigned the number in the text box. The residue numbers for the remaining residues are shifted by the same amount as that of the residue with the lowest number. Renumbering therefore preserves gaps in the residue numbering. If you want to eliminate gaps, select the residues above the gap and renumber them.
To set the name for selected residues, choose Residue Name from the Properties menu, enter the name in the Residue PDB name text box, and then define the residues whose name is to be set, either by picking or by using the common objects button to select predefined atom sets or atom selections, or to open the Atom Selection dialog box and define the residues.
To set the name for selected chains, choose Chain Name from the Properties menu, enter a single letter in the Chain name text box, and then define the chains whose name is to be set, either by picking or by using the common objects button to select predefined atom sets or atom selections, or to open the Atom Selection dialog box and define the chains.
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