I have created fragments with make_frags.pl script using the following command lne:
make_fragments.pl -verbose -nosam -nopsipred -nojufo -samfile UapA_SAM.ss2 -id UapA_ UapA.fasta
where UapA_SAM.ss2 is the SAM-predicted secondary structure in pripred_ss2 format, created in the following way:
ss_pred_converter.py --sam UapA.rdb > UapA_SAM.ss2
The UapA.rdb file has been obtained from ROBETTA server. Is this OK?
The default weight file used for fragment picking by "make_fragments.pl" script is the following:
# score name priority wght min_allowed extras
ProfileScoreL1 700 1.0 -
ProfileScoreStructL1 100 1.4 -
SolventAccessibility 500 0.5 -
Phi 300 3.9 -
Psi 200 0.9 -
No SecondarySimilarity and RamaScore are used. Are these priorities and weights suitable for picking fragments for membrane proteins? If not, could someone please recommend me some modifications?
Thanks in advance,
Isn't there any membrane-guy reading this post?