Biomolecules

Import Biomolecules

You can import RNA, DNA and peptide sequences by navigating to File > Import As or to Edit > Source.

If you would like to use the second method, follow the steps below,

  1. Navigate to Edit > Source.

  2. As the Source dialog opens, navigate to File > Import As or press Ctrl+I.

  3. On the Import As dialog click the Import As radio button.

  4. Select either Peptide Sequence, DNA Sequence, or RNA Sequence.

For more information, see Sequences - peptide, DNA, RNA.

Peptides can be entered by using their 1- or 3-letter amino acid codes.

DNA nucleic acid sequences can be imported in the following formats:

  • ACGT

  • A-C-G-T

  • dAdCdGdT

  • dA-dC-dG-dT

RNA nucleic acid sequences can be imported in the following formats:

  • ACGU

  • A-C-G-U

Display Biomolecules

The sequences are displayed in groupings of 20 residues.

DNA and RNA sequences are displayed with their 1-letter code on the canvas.

Peptides and proteins can be displayed as either their 1-letter or 3-letter codes in MarvinSkecth. Navigate to View > Peptide Display to specify the display mode.

images/download/attachments/1802554/Peptide_Display.png

The View > Colors > Peptide Bridges option color bonds that are crosslinking amino acids in different.

Drawing Bridges and Cycles

You can easily draw peptide bridges and cycles in MarvinSketch.

images/download/attachments/1802554/Peptide_Bridges_Colored.png

images/download/attachments/1802554/Draw_Bridges.png

It makes it easier to visualize bonds between amino acids, disulfide bridges, cyclic peptides, and lactam or lactone structures occurring frequently in peptides and proteins.

  1. Select the single bond tool and drag a bond from an amino acid.

  2. Release the mouse button.

    1. If there is more than one free attachment point on the starting and/or ending amino acid, you must select the appropriate one.

      images/download/attachments/1802554/Select_Attachment_Point_Dialog.png

Delete the explicit H and OH from the terminal amino acids when drawing a head-to-tail cycle.

A bond can be started only from an amino acid that has at least one free attachment point.