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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: 

-fake_native Error - not found in command line of rosetta 3.2.1

Hi All,

So, I am trying to set up my docking experiment between two proteins.
I had read that for blind docking one should use the flag: -fake_native.
When I do this, I get the error: "Option matching -fake_native not found in command line top-level context"

Does this mean that "-fake_native" is no longer a flag option? And if so, is there a flag to replace it?


Post Situation: 


Hi List,
When clustering, I've got thousands of the following warning message: [ WARNING ] Number of atoms in pose and silent file disagree! Attempting to continue ... [ WARNING ] (in residue 287 natoms_pose=7atm_seqpos 287 natoms_struct=11)

Before clustering, I have gathered several silent files using the full atom mode with the option "silent_struct_type binary". Is there something to do with the structure type?

Post Situation: 


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