Question:

How do I generate valid 3D conformations for my molecules?

Answer:

The MarvinSketch web server allows you to draw your molecule and convert it to 3D.
The PRODRG server is another option.
The balloon software also can create 3D atomic coordinates.

Question:

What is the difference between "Features" and "Spatial Features"?

Answer:

Different features, can map to the same point in 3D space. For example, a group can be both hydrogen donor and acceptor. In this case we consider them as 2 features but 1 spatial feature.

Question:

I upload a zip file to the server and get the following message:
Filename 0: structures_mol2
Filename 0: __MACOSX
Only 0 valid molecules were given, please supply at least 3 valid molecules

Answer:

The zip archive you upload should NOT contain any folders, only zipped mol2 files. Additionally, when the files are zipped on Mac, some hidden files and folders are automatically added. Our server can not recognize them as mol2 files. If you use Mac, please zip your files in the terminal window using zip command:
zip input.zip *.mol2