A SYNOPSIS OF THE CAPABILITIES OF THE StruMM3D MODELER
StruMM3D is written for the Microsoft Windows ® environment, and so requires a mouse.
StruMM3D will perform any function that is currently available in any other molecular modeling program.
StruMM3D's "environment control" commands will:
- write atomic symbols onto the structure
- draw hydrogens onto the structure
- number the structure's atoms
- draw covalent radii about the atoms
- visually alter the opacity/color of all atoms, for easier viewing
- switch between line styles for drawing structures, for flexible 3D viewing styles
- activate error-corrected searching for delocalized bonds
- automatically adjust the size of the molecular model to full screen size
- show the charge on an atom, if the molecule has less than 1024 atoms and lone pairs
- automatic saving of the molecule(s) in memory if a structural change occurs
- enable/disable program sounds
These "environment control" settings can be changed to suit your needs, are stored, and are available each time you use the program.
StruMM3D's main commands will enable the user to:
- auto-save the coordinates of the structure(s), same file name,
overwrite old data.
- change the length of a bond
- change an atom type, adjusts new bond lengths
- draw a new structure or modify an existing one
- erase an atom, or group of atoms
- elaborate atoms into full valency, digonal, trigonal or tetrahedral
- erase a structure from the screen
- locate and label aromatic rings
- search for and measure any 4 atom functional group, linear or branched, etc.
- fragment a structure, into two entities (structures A and B)
- screen-dump the model to the printer
- hardcopy (to printer) the atomic coordinates, types and bond lengths
- link two structures on-screen with complete control of all stereochemistry
- dock two, or more molecules under the influences of their intermolecular interactions
- easily locate any atom in a complex structure
- locate and measure all lone pair interactions
- move an atom interactively to alter or minimize its energy
- show the molecular formula(e) of the structure(s)
- measure molecular geometry - lengths, angles, dihedrals
- rotate, translate, the structure in 3 dimensions
- re-orient the structure, putting 2 chosen atoms in the XY plane
- position any atom of a large, difficult-to-view molecule at mid-screen
- rotate about a bond, in 3 dimensions, and minimize the energy of that dihedral angle(see below)
- retrieve coordinate data from a data file, and display the molecule
- reflect, and enantiomerize, the structure about the Z axis
- review all atomic coordinate and structure data
- locate and measure all steric/torsional/polar interactions
- save/write a molecule's coordinates to a disk data file
- query/change the symbolic designation and pi status of an atom
- adjust the structure's size, use up/down cursor keys
- write an XYZ file for the structure that is in memory
- enter basic X-ray crystallographic coordinate data into StruMM3D
- change the display/video type and/or the number of atoms/structure
- identify/select an atom and its coordinates
- access this help file, also use 'help'
- minimize/measure the structure energy of a molecule in memory
- rotate the structure continuously, or stepwise, about the X-, Y-, or Z-axis
StruMM3D possesses many others features that arise from the combined usage of the "tools" described above. The program is heavily prompted to assist the user, using menus in the Windows environment. Users can also copy and paste images of the molecular models into any MS Windows application that will accommodate graphics. This is an excellent way to present your molecular modeling results, IN BOLD COLOR.