Hi Guohui,
Good progress!
Try to finish 'fiber' model building first, as suggested earlier. Present the user with a full-list of available models (55), and based on selected model number, ask for sequence or just repeating unit. It is fine to have the most common A-, B-, C- and Z- (not D-, or with D-) form at the top.
I am not a designer either -- in the 3DNA forum, I have been asking for user's contributions. Until very recently have I updated the 3DNA forum logo. But honestly, I do not like the one you currently post there. I have created an alternative as attached here, which has a transparent background.
For 'analyze', you could pre-build all available NDB entries. Thus when a NDB/PDB id is supplied, the results are immediately available.
Keep good work!
Xiang-Jun
[attachment=0:pn02lib2]w3DNA_logo.gif[/attachment:pn02lib2]