Reply To: Fragment files for membrane_abinitio application

[Anonymous]

Hi,

The span file specifies only approximate positions of transmembrane regions – it does not specify how many residues you will get in a transmembrane helix. The number of residues in a transmembrane helix depends on the secondary structure prediction for that region (that is reflected in the fragments library). I would recommend to try to use only SAM secondary structure prediction file (*.rdb) to generate the fragments – see rosetta3.2 manual:
http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/membrane_abinitio.html,
where we have the following advice:
“Generate structural fragments only using SAM secondary structure prediction file (*.rdb) – jufo and psipred predict transmembrane helical regions poorly.”
If it does not help, then according to the secondary structure prediction methods used by rosetta, that helix is not predicted to contain ~30 residues.