You are here

Home

Unsolved

The problem hasn't been solved

Calibur-linux binary or source code availability?

Submitted by jasnyderjr on Sat, 2016-12-10 23:36
Category: 
Docking

Just wondering if there been any progress toward building the Cailibur program for clustering into RosettaDock?

Is the Calibur source code available anywhere?  All I seem to find is the binary version on the  http://sourceforge.net/projects/calibur/, and I only get this to work on a windows envrionment.  It would be nice to have Calibur version for use on  a Linux platform.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

General protein-protein docking when no info. on structure is availble

Submitted by jasnyderjr on Fri, 2016-12-09 04:55
Category: 
Docking

We plan to follow/advise the following steps for protein-protein docking when no known information on the complex structure is available and, it is necessary to do an initial global search around one partner. 

The objective of clustering is to, ideally, seek larger clusters of decoy structures having more closely spaced energies.

Hence, the following sequence of steps is proposed for protein-protein docking where no known information on structure is available:

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Writing out individual residues to a pdbfile

Submitted by SenyorDrew on Thu, 2016-12-08 07:33
Category: 
PyRosetta

I've recently changed to a more recent version of pyrosetta (upgraded from rosetta_src_2016.18.58680_bundle to  rosetta_src_2016.46.59086_bundle).  One of my scripts no longer works,as it seems I can no longer find the function "dump_pdb_residue".  This function still looks like it exists in the C++ code:

----------------------

In [1]: from rosetta.core.io.pdb import dump_pdb

Post Situation: 
Unsolved
Forums: 
PyRosetta - General

backrub application, resfile, and pivot_residues

Submitted by tylerborrman on Tue, 2016-12-06 14:46
Category: 
Loop Modeling

Hi,

I've been attempting to use the "backrub" app to model mutations while allowing flexibility of the backbone in specific protein stretches.

It appears adding the resfile (with or without mutations specified) causes backbone flexibility across the entire output structure and not restricted to the protein stretches specified by -pivot_residues.

***************************************************************************************************************************************

Example:

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Error compiling on ubuntu 16.04

Submitted by SenyorDrew on Wed, 2016-11-30 13:26
Category: 
Compilation

Hi,

I'm having trouble compiling PyRosetta on Ubuntu 16.04 64-bit

Rosetta version is: rosetta_src_2016.46.59086_bundle

gcc version is 5.4.0

Python version is 2.7.12

Initially I set up PyRosetta for compilation by executing "DeployPyRosetta.py" in  "tools/PyRosetta.develop".  I ran into an issue compiling gccxml, and added the flag "-DCMAKE_C_FLAGS=-fgnu89-inline" to the DeployPyRosetta.py script to get the setup script to run to completion.

Post Situation: 
Unsolved
Forums: 
PyRosetta - Build/Install

Rotamer Library Generation in Rosetta3

Submitted by jcminerlanl on Wed, 2016-11-30 07:34
Category: 
Non-Canonical Peptides

I have been stuck on the problem of generating rotamer libraries for a while now as I try to repeat the process for non-canonical residues (starting with the test case of ornithine [C40]).  The original documentation for this process is provided at the following address:

https://www.rosettacommons.org/demos/latest/public/make_rot_lib/README

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

FloppyTail options error

Submitted by DmitriiN on Fri, 2016-11-11 02:54
Category: 
Loop Modeling

Hello, everyone!

I'm trying to use FloppyTail application, however it always gives me an error:

[ERROR] EXCN_utility_exit has been thrown from: src/protocols/floppy_tail/FloppyTailMover.cc line: 268
ERROR: invalid flexible region (start (0) or stop (0) is undefined) - check your flags or movemap file


I tried to use it with options from the demo (in /integration/tests), and simply running like

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

can't find toolbox module

Submitted by rta on Thu, 2016-11-03 02:22
Category: 
PyRosetta

 

Hi!

I was not sure if this is 'build/install' question, but it seems that 'general' forum is for more advanced issues..

I'm a beginner in PyRosetta and not really a "tech" person, more wet biologist so sorry if the question is stupid..

Currently using tutorial from http://graylab.jhu.edu/pyrosetta/downloads/documentation/Workshop2_PyRosetta_Intro.pdf to try basics of PyRosetta.

Post Situation: 
Unsolved
Forums: 
PyRosetta - Build/Install

Pages