Reply To: questions about ab init membrane protein

[Anonymous]

Answers from a membrane_abinitio developer (in case others need them, I know you already got them albumns):

You need to download blast program (that contains blastpgp) and nr database (protein sequences database) at:

http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download

Blast program and nr database also used to generate fragments – see:

http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/fragments.html

Once you install them, include full paths to their location on the command line for run_lips.pl script.

Best regards,
Vladimir