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Selecting Top Scoring Decoys


I have a silent file of 20,000 decoys and I want to extract/separate low energy decoys out to a separate silent file for all atom relax. Is there any possibility of doing it. I tried cluster.linuxgccrelease with -cluster:output_score_filter and it doesn't seem to work! Is there any workaround or possibilities of any script!

Post Situation: 

ld: cannot find -lz

Dear colleagues,

I am trying to install Rosetta 3.3 on:

- HP ProLiant DL380 G6
- CPU: 2 x Intel Xeon Quad Core
- OS = SUSE SLES 11, kernel, x86_64
- compiler: gcc 4.3-62.198-x86_64
- python: 2.6.5
- scons: 2.1.0

command: scons bin mode=release

crash + error message:

/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/lib/ when searching for -lm
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm

Post Situation: 

PyRosetta Initial Setup

Mac OSX 10.7 - Lion 64bit
Python v2.7.2
PyRosetta 2.0

I downloaded and extracted the files for PyRosetta. I moved them to my documents. When I open terminal and go the directory where PyRosetta is located I cannot step 4 to work from the instructions online.
4. From within the PyRosetta directory, type 'source' into the command line to set up the PyRosetta
library filepaths"

I type "bash-3.2$ source"

I receive an error that says "bash: cd: not a directory

Post Situation: 

Energy updates in Rosetta 3.3

Trying something like the following in C++ Rosetta 3.3:

P = new core::pose::Pose();
Q = new core::pose::Pose();

scoreFxn(P); //-501.22
scoreFxn(Q); //-528.17

for(size_t k=1; k<=P.n_residue(); k++)

  • P.set_phi(k,Q.phi(k));
  • P.set_psi(k,Q.psi(k));
  • P.set_omega(k,;

scoreFxn(P); //3826.51

Post Situation: 

Enzyme design with variable CST blocks possible?

I am wondering if it is possible to use the enzyme design algorithm with a cst file containing variable cst blocks used for matching. I am using the following cst file for my matching:

#block 1 - Malimide-Cys
TEMPLATE:: ATOM_MAP: 1 atom_name: C1 C2 H1
TEMPLATE:: ATOM_MAP: 1 residue3: HAS

TEMPLATE:: ATOM_MAP: 2 atom_name: SG CB CA
TEMPLATE:: ATOM_MAP: 2 residue1: C

CONSTRAINT:: distanceAB: 1.85 0.20 240.00 1 1
CONSTRAINT:: angle_A: 105.00 10.00 58.00 360.00 1

Post Situation: 

-kill_hairpin error


I'm trying to use the Abinito application, and I keep getting a kill_hairpin error when I use the .psipred_ss2 file generated with fragments in robetta. Has anyone experienced this? I'm using rosetta3.3 (newest).
I'm also using the flag -psipred_ss2 with no errors...and...Both point to the same .psipred_ss2 file.
This is the error:
ERROR: [ERROR] Unknown file type for kill_hairpins file (need psipred_ss2 or kill)
ERROR:: Exit from: src/core/scoring/ line: 358



Post Situation: 


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