Fragments Panel

This panel provides a wide range of fragments, grouped into libraries, that you can use for building or adding to structures.

To open this panel, click Add Fragments in the 3D Builder Panel panel, then click More.

  • Using
  • Features
  • Additional Resources

Using the Fragments Panel

Adding a fragment from the Workspace

To add a fragment, first select the atoms in the Workspace that you want to add the fragment to, then select a fragment library from the Fragments menu, then select a fragment. The fragment is immediately added to the selected atoms. When you select multiple atoms, the same fragment is added to each one. If no atoms are selected, the fragment is placed in the Workspace where you click as a separate molecule; if there is more than one entry in the Workspace, you are prompted to choose the entry to add the molecule to.

Fragments Panel Features

Fragments option menu

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 fragment display area. The available libraries are:

These libraries are described below. In addition, there is a Recent item, which displays the most recently used fragments, given by name.

Organic

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.

Rings

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.

Heterocycles

The four heterocycle fragment libraries provide a range of ring structures that contain nitrogen, oxygen, and sulfur atoms.

Furanose and Pyranose Structures

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.

Metal Centers and Ligands

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, right-click on the metal atom, choose Elements from the shortcut menu, then select the desired metal.

Amino acids, DNA, RNA, and Protein capping groups

The Amino acids library contains the 22 naturally-occurring amino acids. 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.

Nonstandard 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. There are two sections: Built-in and Custom amino acids. The Built-in section contains nonstandard amino acids provided in Maestro by default, while the Custom nonstandard amino acids section contains custom entries added by the user. Click the header label of a section to collapse or expand it.

Double Stranded DNA
The Double Stranded A DNA library contains deoxyribonucleic acid base pairs in the A helix conformation: A:T, T:A, C:G, and G:C. The Double Stranded B DNA library contains deoxyribonucleic acid base pairs in the B helix conformation: A:T, T:A, C:G, and G:C. The Double Stranded A RNA library contains ribonucleic acid base pairs in the A helix conformation: A:U, U:A, C:G, and G:C. The Double Stranded B RNA library contains ribonucleic acid base pairs in the B helix conformation: A:U, U:A, C:G, and G:C.
Protein ions & solvents

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.

Diverse fragments

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.

Fragment display area

Displays the fragments from a library. Some fragment libraries are displayed as 2D structures, others are displayed as names.

Fragment type option menu

This option menu is displayed for the carbohydrate libraries, and provides alpha and beta options.

Include capping groups option

Include capping groups when adding an amino acid fragment. Available for both standard and nonstandard amino acids. Deselect this option to add amino acids without capping groups.

Move selection for chaining option

Move the selection to the designated leaving atoms on the fragment so that a chain can be built. Only available for standard amino acids.

Options button

Show or hide options for joining geometry and secondary structure. Only available for standard amino acids.

Joining geometry option menu

Specify the joining geometry of the current fragment with respect to the previous fragment. The options are cis and trans. Only available for standard amino acids.

Secondary structure option menu

Specify the kind of secondary structure to be built. You can choose various helix and sheet arrangements, as well as extended structures, or choose to set custom phi and psi angles. For custom angles, you are prompted to set the angles on each fragment addition. Only available for standard amino acids.

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