Build Biopolymer from Sequence Dialog Box

Build a biopolymer from a sequence, with options for control of the secondary structure.

To open this dialog box, choose Other Edits → Build Biopolymer from Sequence in the 3D Builder panel, or click the Tasks button and browse to Protein Preparation and Refinement → Build Biopolymer from Sequence.

  • Features
  • Additional Resources

Build Biopolymer from Sequence Dialog Box Features

Biopolymer type option menu

Choose the type of biopolymer to build, from Peptide, DNA, or RNA. The choice affects the features that are displayed.

Title text box

Specify the entry title for the new project entry to be created for the biopolymer.

Sequence text box and browse button

Specify the biopolymer sequence in this text box, or click the browse (...) button to locate and read a file that contains the peptide sequence. You can copy and paste sequences into the text box.

If the biopolymer is DNA, a second, noneditable text box is displayed below this text box. This text box shows the complementary sequence to the one specified.

Shape option menu, text box, and browse button

Choose the type of secondary structure to build the biopolymer in. You can choose from a list of standard secondary structure types for peptides, or helix conformations for DNA or RNA.

For peptides, you can provide custom information with the following items:

  • Custom Secondary Structure Assignment—specify the secondary structure assignment (SSA) for the sequence by entering a letter code for each residue that defines the secondary structure element. The letter codes accepted are H for helix, E for strand, and C, ~, or - for loop (coil). You can also read the SSA from a file, by clicking the browse (...) button and browsing to the file, which must be a sequence file in FASTA (.fasta), SEQ (.seq), or plain text (.txt) format. If the sequence is not yet specified and you read a file that contains both a sequence and an SSA, the sequence is read in as well as the SSA.

  • Custom Angles—specify the phi and psi angle for each residue in a comma-separated list, in the order in which the sequence is given, i. e. as phi1,psi1,phi2,psi2, ... . You can also read the angles from a file, by clicking the browse (...) button and browsing to the file, which must be a sequence file in FASTA (.fasta), SEQ (.seq), or plain text (.txt) format. If the sequence is not yet specified and you read a file that contains both a sequence and an angle list, the sequence is read in as well as the angles.

Build double-stranded option

Build double-stranded DNA rather than a single strand. This option is only available for DNA.

Build button

Build the biopolymer. The Workspace is cleared, the new biopolymer is displayed in the Workspace and is added to the project as a new entry with the specified title.

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