You are here

Home

Unsolved

The problem hasn't been solved

Capturing the output of scorefxn.show(pose)

Submitted by ajasja on Fri, 2014-06-20 05:30
Category: 
PyRosetta

I'm using PyRosetta-r21 on Ubuntu togather with IPython 2.0.0 notebooks. This works extremly well, with one small problem:
Some output is redirected to the console in which "ipython notebook" command was started instead of the notebook cell. 
So the question is: is it possible to capture the output of scorefxn.show(pose)?

I have tried to use the example in "test/T007_TracerIO.py"

 

Post Situation: 
Unsolved
Forums: 
PyRosetta - General

Possible minor mistakes in SetPyRosettaEnvironment.sh (in r21 for Ubuntu)

Submitted by ajasja on Fri, 2014-06-20 05:10
Category: 
PyRosetta

Dear all,
There may be some minor mistakes in the SetPyRosettaEnvironment.sh in the r21 release of PyRosetta:

On line 34 "export LD_LIBRARY_PATH=$PYROSETTA/rosetta${LD_LIBRARY_PATH+:$LD_LIBRARY_PATH}"
$PYROSETTA is not added to the LD_LIBRARY_PATH and "libboost_python.so.1.55.0.so" is consequently not found.
Corrected: "export LD_LIBRARY_PATH=$PYROSETTA:$PYROSETTA/rosetta${LD_LIBRARY_PATH+:$LD_LIBRARY_PATH}"
(Or just move the offending so to rosseta subdir)

 

Post Situation: 
Unsolved
Forums: 
PyRosetta - Build/Install

Approximating CHARMM energy by the rosetta scoring function

Submitted by ajasja on Fri, 2014-06-20 02:16
Category: 
Scoring
PyRosetta

Is it possible to approxmate the CHARMM energy (function) by the rosetta scoring function?

As a starting point I could work with fixed angles and bond lengths, so I guess setting the weghts for fa_atr, fa_rep and fa_elec to 1 and all the rest to zero is a good start. But is it possible to somehow load the CHARMM diheral parameters?

Thank you for your help,
Ajasja Ljubetič

Post Situation: 
Unsolved
Forums: 
PyRosetta - General

Cluster decoys after running PlexPepDock

Submitted by phanvy on Thu, 2014-06-19 06:03
Category: 
Docking

Hello everone

After running the Plexpepdock, I have 40000 decoys. I try to use the cluter program of Rosetta 3.4 . But, I do not understand the meaning of cluster. Because , after I tried to run with 200 decoys and get the out:file with 200 file c.0.XXX.pdb format. I do not understand how cluster work.

Flags:
-in:file:silent decoys.silent
-database /home/tuongvy/SW/rosetta3.4/rosetta_database
-in:file:fullatom
-score:weights
-score:patch
-cluster:sort_groups_by_energy

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Phenix-Rosetta integration tests

Submitted by sansari on Wed, 2014-06-18 15:42
Category: 
Phenix / MR Rosetta

Hi there,

I'm a HPC systems administrator trying to setup Phenix and Rosetta for use with MR Rosetta. I find that the MR Rosetta test suite (phenix_regression.wizards.test_command_line_rosetta_quick) fails at test_fixed_model with the following error in Rosetta:

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Build/Install

Error runining PyRosetta "undefined symbol: __sinh_finite"

Submitted by ajasja on Wed, 2014-06-18 08:09
Category: 
PyRosetta

Hi all!
*OS*: Mint Linux 17,
64bit Linux (3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
*Python*: Python 2.7.7 |Continuum Analytics, Inc.| (default, Jun 2 2014, 12:34:02) [GCC 4.1.2 20080704 (Red Hat 4.1.2-54)] on linux2
*PyRosseta*: PyRosetta.Ubuntu-12.04LTS.64Bit.devel-r56795

While trying to import PyRosseta I get the following error:
"ImportError: rosetta/libmini.so: undefined symbol: __sinh_finite"

Post Situation: 
Unsolved
Forums: 
PyRosetta - Build/Install

MPI nodes hanging and output log incomplete

Submitted by yuvals on Wed, 2014-06-18 05:40
Category: 
Scoring

I'm using MPI with the PeptideDeriver pilot app (which I reworked to support JD2). I am running into some problems:

1. nodes that have finished jobs stall with 100% cpu usage while the entire MPI run isn't complete.
2. some tracer.log files don't contain all of the output -- for instance, the master node might have gotten a success message from a node, but not all the output of that job appear in the tracer.log file (the last bit is missing)
3. some jobs aren't finishing.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Pages

Subscribe to RSS - Unsolved