Hi,
I'm not sure, but I think I've figured out a way how to do what you want.
"Listing S2" in the supplementary information of the original Protter publication was helpful.
First, run the protein sequence at TMHMM 2.0 server, with "One line per protein" as output format.
Then, you can get the result as below.
AVZ43932.1 len=256 ExpAA=152.38 First60=22.70 PredHel=7 Topology=i21-43o58-80i101-123o128-147i160-182o192-211i232-254o
Second, using the protein sequence and TMHMM output, build a kind of web address to access Protter web service.
http://wlab.ethz.ch/protter/create?
seq=MAKPTVKEIKSLQNFNRIAGVFHLLQMLAVLALANDFALPMTGTYLNGPPGTTFSAPVVILETPVGLAVALFLGLSALFHFIVSSGNFFKRYSASLMKNQNIFRWVEYSLSSSVMIVLIAQICGIADIVALLAIFGVNASMILFGWLQEKYTQPKDGDLLPFWFGCIAGIVPWIGLLIYVIAPGSTSDVAVPGFVYGIIISLFLFFNSFALVQYLQYKGKGKWSNYLRGERAYIVLSLVAKSALAWQIFSGTLIPA&format=pdf&numbers&
nterm=intra&
tm=21-43,58-80,101-123,128-147,160-182,192-211,232-254
(1) seq: the full protein sequence (the same as TMHMM input)
(2) nterm: "intra" if the TMHMM result topology starts with "i". Else (starts with "o"), then "extra".
(3) tm: use the TMHMM result topology after editing. (Delete starting and trailing i or o. Replace all internal i or o with comma.)
Third, copy and paste the above web address into the address bar of your web browser, and then press enter. You will get a pdf file (in this case).
Best regards,
Ilnam