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Learning Center
Would you like to…
… learn more about how to use the molecule editor in SYNTHIA™?
Our Molecule Editor is called Ketcher. Like other Molecule Editors, you can quickly draw your structures using bond and atom tools.
Select your bond types and atoms from the corresponding icons in the Editor. There is also a bar of templates for simple rings at the bottom of the editor.
The structure library icon on the right side of the bottom bar allows you to easily access common functional groups, libraries of complex rings and natural product templates.
Note: Only draw exact structures to submit for analysis. SYNTHIA does not recognize query bonds or query atoms for target molecules.
Keyboard Shortcuts
Keyboard shortcuts can be useful to accelerate structure drawing. Here is a list of commonly used shortcuts:
Keyboard Shortcut |
Function |
|---|---|
1 |
Single/Up/Down/Wiggly bonds (keep pressing 1 to toggle between the different options) |
2 |
Double bond |
3 |
Triple bond |
4 |
Aromatic bond |
esc |
Lasso/Rectangle/Fragment Selection tool (keep pressing esc to toggle between the different options) |
t |
Ring template (keep pressing t to select the desired ring in the template bar) |
h |
Hydrogen atom |
c |
Carbon atom |
n |
Nitrogen atom |
o |
Oxygen atom |
f |
Fluorine atom |
Shift+c |
Chlorine atom |
b |
Bromine atom |
i |
Iodine atom |
p |
Phosphorus atom |
s |
Sulfur atom |
Shift+b |
Boron atom |
Import Structures
You can paste structures drawn with other Molecule Editors in SYNTHIA. The Molecule Editor easily recognizes common structure formats, such as:
- SMILES
- MOL text
- InChi
Simply copy the molecule from the other editor and paste it directly into the editor drawing space in SYNTHIA™. If you experience issues pasting structures from a different Molecule Editor, please copy your molecule as SMILES and paste it into the SYNTHIA™ editor drawing space or in the SMILES textbox under it using crtl+v.
Atom Properties Menu
When the selection tool is active, double click on any atom to open the Atom Properties menu. Type an element abbreviation in the ‘Label’ textbox to change the selected atom to this element. This menu can also be used to modify the charge or the isotope of the selected atom.
For isotopes, type the applicable number in the ‘Isotope’ textbox. For example, to get a 13C isotope, type 13 in the ‘Isotope’ textbox with C as Label, or to get a deuterium, type 2 in the ‘Isotope’ textbox with H as Label.
To modify an atom’s charge, type the corresponding number in the ‘Charge’ textbox. For example, to get a positively charged atom, type 1 in the ‘Charge’ textbox. For a negatively charged one, type -1 in the ‘Charge’ textbox. You can also select the charge tools in the left bar and click on the atom which needs to be modified.
Bond Properties Menu
When the selection tool is active, double click on any bond to open the Bond Properties menu. This is useful to build a disconnection strategy for SYNTHIA.
To tell SYNTHIA to avoid any pathways with reactions forming the selected bond, select ‘Not Center’ in the dropdown menu for Reacting Center. This bond will be marked in the editor with an X to indicate it is not a reaction center.
To tell SYNTHIA to favor pathways with reactions forming selected bond, select ‘Center’ in the dropdown menu for Reacting Center. This bond will be marked with a # to indicate it is a preferred reaction center.
