Reply To: P(Res | phi,psi )

[Anonymous]

Hi Jared,

In standard rosetta runs, only the P_AA_pp file is read as input. If you include the “-correct” flag, then instead the P_AA_pp_08.2009 file is read. You can specify an alternate file to read with the “-corrections::score::p_aa_pp ” flag.

The format for this file is non-obvious and most readily understood from the code that reads the file. Look in src/core/scoring/P_AA.cc at the function beginning on line 157. In particular, lines 188/189 actually read from the input stream. The format is something like:

PHI PSI AA3LETTERCODE COUNTS COUNTSTOTAL PROBABILITY

where “COUNTS” and “COUNTSTOTAL” both end up getting ignored by the code. The column widths are fixed.
4 characters for phi,
1 space
4 characters for psi
1 space
3 characters for the aa 3letter code
17 spaces
7 characters for the probability
Hope this helps.

Andrew