Import to BioEddie

This section contains procedures for inserting biomolecules into the Editor.

Render a molecule by any of these methods :

• Imported formats

  • MDL Molfile

  • HELM

    • HELM 1.x

    • HELM 2.x

• Plain Sequences

• Type/Paste a sequence

• Type/Paste multi-letter sequences

• Load from a file

With the Import dialog simple sequences can be typed/pasted directly as text and imported after specifying the sequence type.

All other supported import file formats require you to select a file from a file picker dialog.

{primary} Importing sequences or structures that contain more than 1000 monomers is limited.

Imported formats

• MDL Molfile

• HELM 1.x

• HELM 2.x

• Plain Sequences

• Multi-letter abbreviation Sequences

Natural and unnatural nucleic acid or peptide sequences can be loaded directly.

A fresh installation of BioEddie supports the default 20+2 natural amino acids, the default 5 nucleotides for RNA/DNA and their respective "Any/Unknown residue" placeholders X and N.

The string should contain only one sequence at a time.

MDL Molfile

MDL Molfiles (v2000) can be imported using ChemAxon’s Biomolecule Toolkit product (not part of BioEddie standalone). In case the Biomolecule Toolkit server is not installed or cannot be reached an error message will be shown and the import will fail.

During conversion, the chemical graph of the source MOL file is scanned and reconstituted from a combination of monomers stored in the monomer library. After that, linear sequence backbones and their chemical modifications are identified to compute a HELM-compatible representation. Fragments of the original chemical structure which could not be found in the monomer library will be represented as in-line SMILES monomers.

HELM

For general reference and version specification please consult the home page of the HELM project of Pistoia Alliance at https://www.pistoiaalliance.org/projects/current-projects/helm/

In the seminal paper „HELM: A Hierarchical Notation Language for Complex Biomolecule Structure Representation” published in J. Chem. Inf. Model., 2012 52(10) pp 2796-280 T. Zhang and his co-authors describe this format and demonstrate its application for various types of biomolecules.

Note that not all representation features are currently implemented in BioEddie as listed below.

HELM 1.x

• Basepairings are ignored on import

HELM 2.x

Supported features

• BLOBs as monomers

• bond position ambiguity (?:R and [abbr]:R)

• Attachment point ambiguity (R?)

• Molecule and component level annotations

Unsupported features

• Basepairings on importGroups

• Inline component labels

• Monomer-level ambiguity in components

• Component- and bond-level composition ambiguity

Plain Sequences

Natural nucleic acid and peptide sequences can be loaded directly.

A fresh installation of BioEddie supports the default 20+2 natural amino acids, the default 5 nucleotides for RNA/DNA and their respective "Any/Unknown residue" placeholders X and N. The string should contain a single sequence, eventual whitespaces and numbers are stripped if inserted from the clipboard.

Type/Paste a sequence

1. Click the button.

2. Select the Paste sequence tab.

3. Select a sequence type from the dropdown list. Peptide and nucleic acid sequences are supported currently.

4. Type or paste the sequence into the text box.

5. Click " Load ".

If there are other components on the canvas, the newly inserted sequence will be aligned to the left of the canvas.

{warning} Upon pasting, numbers and whitespaces occurring in the sequence get omitted.

Invalid characters for the chosen sequence type are highlighted in red and an error message will appear by placing the cursor in front of the invalid character.

Type/Paste multi-letter sequences

1. Click the button.

2. Select the Paste multi-letter sequence tab.

3. Select a sequence type from the dropdown list. Peptide and nucleic acid sequences are supported currently.

4. Type or paste the sequence including '.' separators before or after the monomer abbreviations into the text box.

5. Click " Load ".

If there are other components on the canvas, the newly inserted sequence will be aligned to the left of the canvas.

Load from a file

1. Click the button.

2. Select the From file tab.

3. Choose the file type from the dropdown box.

4. Navigate to the location of the file of interest and select it.

5. Click " Load ".

Loading a file clears the canvas, only the content of the newly loaded file will be displayed.

{info} Once you have selected a file, the corresponding .mol or .helm file's content will appear in the Import dialog's editor box. Here you can modify the content by typing prior to loading it.