Build Menu
Contents |
Change H to Methyl
Add Hydrogens
Add Hydrogens for pH...
Will add or remove acidic hydrogens according to the desired pH.
Only (?) affects ionizable groups in peptides: carboxylic acid, amine, imidazole, guanidine, phenol.
Guanidine and phenol don't seem to be affected when not part of a peptide.
Remove Hydrogens
Insert
Fragment ...
- Choose a molecule to insert from the fragment library.
You may need to navigate to the share/avogadro/fragments directory first (Windows)
- Select the folder containing the functional group you want to add.
- Click the desired molecule.
- Click the Insert Fragment button.
- Close the fragment window by clicking the X in the top right corner.
You can add more than one fragment at a time. Caution: each fragment will appear in the center of the window, you will have to move them to prevent the molecules overlapping one another.
SMILES...
Type a SMILES string into the textbox and click OK
Peptide...
Opens the peptide builder window.
You can build peptides from the 20 standard amino acids by either clicking the buttons or typing the three-letter codes for the desired amino acids separated by hyphens. The one-letter codes are not understood by the builder.
For example: Gly-Ala-Cys
Additional settings are available for:
- Structure: straight chain, Alpha helix, beta sheet, other
- Phi and Psi angles
- Stereochemistry: D or L
- Ionization state of the C- and N-termini
