Hi!

You can't create detailed PDB-like 3D structure from just a sequence or alignment. This task is a big challenge for a lot of researchers today and there are no reliable solution still.

You have 2 options with UGENE:

1) If you know the protein/family encoded in you FASTA or ALN file you can use the protein name to fetch the 3D structure from PBD database. Just use File->Access remote database menu, select PDB and type in the name.

2) Use secondary structure prediction methods available in UGENE (GOR/PSIPRED) to locate certain secondary structure regions in the sequence. But it won't give you 3D image.