Unsolved

PSSM(position-specific scoring matrix) is a commonly used representation of motifs in biological sequences, and psiblast to generate a PSSM. a portion of a PSSM shows as follow:
A R N D C Q E G H I L K M F P S T W Y V
1 G 0 -2 0 -1 -2 -2 -2 5 -2 -4 -3 -1 -3 -3 -2 0 -2 -2 -3 -3
2 S 0 -1 4 1 -2 0 0 0 0 -3 -3 0 -2 -3 -1 3 1 -3 -2 -2
3 G 1 -2 0 -1 -2 -1 -1 5 -2 -3 -3 -1 -2 -3 -2 2 0 -3 -3 -3

Hi all,

I am trying to implement the method outlined in "Incorporation of Noncanonical Amino Acids into Rosetta and use in Computational Protein- Peptide Interface Design" doi:10.1371/journal.pone.0032637.

I just wondered if I should start right from the beginning, or whether there is somewhere I can download the parameter files, rotamer libraries and unfolded state reference energies for NCAAs so that I can move directly to doing the design protocol.

Any advice would be most appreciated.

wsgosal

Dear Rosetta users:

I ran a full structure prediction on the Robetta web server and obtained useful results. Now I would like to run Rosetta locally (because I want to control the fragment libraries).

I installed Rosetta3.5 and did a test run, but the locally-generated structures are quite different than those that I obtained from the Robetta web server (the Robetta results are much better). I presume that this is because I have not configured the local Rosetta run very well.

Hi all,
Just a heads up. There's a problem linking with the new OSX Command Line Tools and clang version 5.1.
This is with the most recent weekly release 2014 week 04
Any suggestions would be appreciated

Clang version:
clang --version
Apple LLVM version 5.1 (clang-503.0.38) (based on LLVM 3.4svn)
Target: x86_64-apple-darwin13.1.0
Thread model: posix

Error message

Undefined symbols for architecture x86_64:
"core::io::silent::ProteinSilentStruct_Template::fill_struct(core::pose::Pose const&, std::string)", referenced from: