I know there are several free scripts to import the data, but it replaces the structure with some other primitives like spheres. but I need the structure from the molecule as such (see the link above). is there a way to import this in max?
as far as I know none of the native max or maya readers does other structures than sticks and balls. If you want to have rubber bands or something like that you have to use a standalone viewer and export to vrml.
The ones I know of are:
Weblab Pro
MDLChime
MolVRML
jmol
spdbv
If you search on google for them you should find links
So in case you have an application that displays the model the way you want but doesn’t offer a way to export the 3d-geometry - try OGLE to create a .obj file. OGLE only works if the OpenGl application doesn’t make use of display-lists (for example capturing a model in the application Cn3D doesn’t work because of this).