MarvinSketch assigns the following stereochemical notations:
(R), (S), (r), (s) for tetrahedral stereochemistry
(E), (Z) for cis-trans isomerism
(M), (P) for atropisomers
These notations are calculated automatically, MarvinSketch updates them as you change your molecule.
The display of the individual stereochemistry indicators can be set in the View > Stereo submenu.
The relative position of ligands on a chiral atom is marked with wedge bonds: up (solid ), down (hatched), up or down (wiggly ).
Having wedge bonds at chiral atoms with the chiral flag on the entire structure implies that a single isomer is present. The absolute configuration (R or S) is known for all chiral centers that are marked with wedge bonds.
Non-stereo bond to atom at stereogenic centers implies that no information is known about the configuration of a stereogenic center. It could be either of two stereoisomers or a mixture of the two.
The absolute configuration of a chiral molecule can also be defined by using Structure Menu.
The existence of wedge bonds at chiral atoms without a chiral flag on the entire structure has two meanings depending on the file format used.
MDL file types (MOL, SDF ): The structure is a racemic mixture of the two enantiomers.
Daylight file types (SMILES, SMARTS): Wedges mean the absolute stereo configuration, the structure represents a single enantiomer.
The positions of the double bond ligands already define the stereo configuration of the double bond (cis or trans). Special query double bond types allow us to specify cis or trans, not trans or not cis isomers.
Axial Stereoisomerism - Atropisomerism
Atropisomers are drawn with solid wedged and hashed wedged bonds within the aromatic rings and directly connected to the single bonds about which they rotate.
Enhanced Stereo Specification
Enhanced stereochemical representation introduces three types of identifiers that can be attached to a stereogenic center. A stereochemical group label is composed of an identifier and a group number. Each stereogenic center marked with wedge bonds belongs to one (and only one) stereochemical group. Grouping allows us to specify relative relationships among stereogenic centers.
A stereogenic center where the absolute configuration is known.
A Stereogenic center where the relative configuration is known, but the absolute configuration is not known. The structure represents one stereoisomer that is either the structure as drawn (R, S) OR the epimer in which the stereogenic centers have the opposite configuration (S, R).
A mixture of stereoisomers. It can be a pair of enantiomers or all the diastereomers.
You can find more information on the scientific background of stereochemistry here.