Most people don't like to read extensive manuals - and good programs should not require people to do so. Therefore this experiment of a shortest possible manual. It avoids lengthy descriptions of things which are obvious to most people. Please also read the document "About ChemViewer3D" to complete your information.
Of course, the program offers many more features than the ones described below. If you'd like to explore the full potential of the program, the simplest advice might also be the very best: try all available menu commands and observe how they act on a model. This will let you experience these actions in a straightforward 1:1 fashion.
How editing works
All changes to a model are accomplished in the same basic manner: first select the desired atom(s) by clicking it/them or by dragging the mouse over the desired area. All properties offered by the "Selection" menu can then be applied to the selection.
Additional selection options
The selection menu also contains options for getting geometric info of the selected atom(s) (location, distance, angle, dihedral angle). These commands are only vaild if 1-4 atoms are selected. You can also select further atoms in a specific range relative to a selected atom (sphere, front, back, radius, same molecule). In this case, exactly one atom has to be selected as a reference.
Interactive animation
Interactive animaton is performed by pressing a specific keyboard key (SHIFT for translation, ALT for rotation, CTRL for light source) while moving the mouse and optionally pressing the mouse button for some functionalities. Please refer to the "Animation Help" item in the Animation menu for complete information.
Move to specific orientation
Models can be moved to satisfy specific viewing criteria. They may be aligned for the closest distance of a selected atom to the viewer, a view into the direct connection line of two selected atoms, and finally for a perpendicular view on the plane defined by three selected atoms. 1-3 atoms must be selected for these commands. An animation moves the model to desired position.
Backgrounds
Optionally, background pictures (the provided ones or your own PICT files) can be imported via file menu => backgrounds. To keep the size of the model files small, only a reference to the picture on your local drive is saved, not the picture itself. If you provide somebody else with a model file containing a self made custom background, don't forget to provide him with the corresponding picture file, which should be put in the "Backgrounds" folder on the new machine.
Import formats
For the specification of the three main import formats accepted by ChemViewer3D, please refer to the examples located in the import folder. ChemViewer3D recognizes practically all flavours of the coordinate format automatically. The two versions of the MicroWorld format are fully supported (MW and MW+; the latter incorporates explicit connections).
ChemViewer3D takes advantage of most available information (eg. structural elements, chains, and so on) contained in PDB-files. These contain protein data and are distributed by the Brookhaven Protein Database, which is accessible from the Net. To download, go to "ftp://ftp.pdb.bnl.gov/index/compound.idx" and get the internal ID-code of the desired protein. Then go to "http://www.pdb.bnl.gov/pdb-bin/ browse" and enter the ID-code in the browser in order to download the corresponding PDB-file.
