Apologies for what i am sure are the rantings of a novice blender user. I have the latest version (on mac) and am having problems getting chemical structures into blender. I draw these (for example in something like chemdraw) then convert into pdb files then import - these appear in blenders as disconnected "balls" that are rather difficult to manipulate, join etc. The pdb files are fine - i can open and check them in macPymol. Any advice really welcome.
Blender in a graphic program, and does not know chemistry.
In order to build (chemical) links, what is needed is a library, or some other means to let Blender know which atoms are connected to which. Then you will have to select the kind of joint to be used as link.
What do you use to read and import the pdb file?
If your molecule is a biological molecule (protein or nucleic acid, or sugar) you could use [url]BioBlender.net[/url], that contains the reader and the libraries (plus some other features).
Hope this helps,