Mouse Modes
SEQCROW's mouse modes can be found on the "More Right Mouse" tab of ChimeraX's toolbar or activated using the mousemode command.
Select all atoms with a connectivity path to the atom, bond, or residue that was clicked. Regular clicking will toggle whether that fragment is selected. So, clicking an atom that is selected with deselect everything connected to it, and clicking an atom that is not selected with select the molecular fragment. Using shift+click will deselect everything else, causing only the clicked fragment to be selected.
Clicking and dragging will select fragments with atoms, bonds, or residues in the box lasso.
Click and drag from one atom to another to draw a bond between the pair of atoms. Clicking a bond will delete the bond.
Click and drag from one atom to another to draw a forming/breaking bond between the pair. Clicking a bond will replace the bond with a TS bond. Clicking a TS bond will delete it and replace with a normal bond if it reasonable to do so (i.e. bond atoms reasonable true).
The element can be set by clicking for the first time, or by shift-clicking. This will pull up a periodic table for choosing the element and a shape option for choosing the geometry. If the "keep table open" option is checked, this window will stay open and continuously update what element and VSEPR the mouse mode uses. If the box is unchecked, the element and VSEPR will only be set when set element and shape is clicked.
Clicking an atom will change its element and shape what has been selected on the periodic table as long as it is reasonable to do so. For example, a quaternary carbon cannot be changed to a trigonal planar carbon because it has too many bonds to heavy atoms. One or more fragments would have to be removed before making this change.
Atoms and bonds can be deleted by clicking on them or clicking and dragging over them.
The substituent can be set by clicking for the first time, or by shift-clicking. This will pull up a table with all available substituents. A substituent is selected by highlighting the corresponding row on the table. There are also options for putting the new substituent atoms in their own residue ("new residue"), changing the residue name ("set residue name"), and using remoteness labels for the atom names ("distance atom names"). If the "keep list open" option is checked, the substituent info will be continuously updated. If the option is unchecked, the substituent info will only be updated when the set substituent box is checked.
To change a substituent, click on an atom. The longest fragment bonded to that atom will be kept, and the new substituent will replace the clicked atom.