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(drluca77) python/gcc combo for mac build, pyrosetta 2.0

(This comment copied from a different topic)

Hello.

I downloaded and tried to use the Mac version, but I get this error:

Python 2.6.5 (r265:79063, Mar 20 2010, 11:39:18)
[GCC 4.2.1 (Apple Inc. build 5646) (dot 1)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from rosetta import *
Traceback (most recent call last):
File "", line 1, in
File "rosetta/__init__.py", line 11, in
import utility
File "rosetta/utility/__init__.py", line 1, in
from __utility_all_at_once_ import *

Post Situation: 

3.2 with Intel Compilers on OS X Intel

Is building Rosetta 3.2 with the Intel compilers on OS X Intel supported? I ran the build like so:

./scons.py bin mode=release cxx=icc

And the resulting commands look like this:

g++ -o build/src/release/macos/10.5/64/x86/icc/super_aln.macosiccrelease build/src/release/macos/10.5/64/x86/icc/apps/public/comparative_modeling/super_aln.o -Llib -Lexternal/lib -Lbuild/src/release/macos/10.5/64/x86/icc -Lsrc -L/usr/local/lib -L/usr/lib -ldevel -lprotocols -lcore -lnumeric -lutility -lObjexxFCL -lz

Post Situation: 

3.2 and Intel Compilers 12.0

It looks like there is some buggy interaction between Rosetta, Scons and the latest version of the Intel compilers.

I edited tools/build/options.settings to enable the 12.0 compiler version and tools/build/user.settings to find the Intel compilers and the error looks like this:


$ ./scons.py bin mode=release cxx=icc extras=static tatic
scons: Reading SConscript files ...
svn: '.' is not a working copy
scons: done reading SConscript files.
scons: Building targets ...

Post Situation: 

Rosetta parallel installation

Hi all,
have been using Rosetta for a while, but could not figure out exactly how to install parallel. I am very happy to see Rosetta3.2 latest version. I will be grateful to you if anyone suggest me how to install (best way)parallel and how to run applications in parallel.

Thank you in advance

Best regards,
vamsi

Post Situation: 

Rosetta 3.2

I used pc with Fedora 14. I used gcc 4.5 and mpich2 to compile Rosetta 3.2. However I encounter this erros when I try to compile Rosetta 3,2 with scons.

src/core/conformation/symmetry/util.cc: In function 'void core::conformation::symmetry::make_symmetric_pose(core::pose::Pose&, core::conformation::symmetry::SymmetryInfo)':
src/core/conformation/symmetry/util.cc:360:37: error: expected type-specifier
src/core/conformation/symmetry/util.cc:360:37: error: conversion from 'int*' to non-scalar type 'core::pose::PDBInfoOP' requested

Post Situation: 

unable to propagate location of libraries to scons for Rosetta 3.1 [FIXED...SORT OF...]

I am unable to propagate our cluster environment to the Rosetta scons scripts (most likely the library environment)

Here is my situation:

On our cluster, compilers are loaded using "module" (e.g. "module load compilers/gcc/4.4.2" or "module load mpi/openmpi/1.4.3_gcc").
-> Consequently, compilers (gcc, g++, ...) are not in "normal" PATH, and the same goes for some required libraries (and for INCLUDE paths also)

Post Situation: 

Docking an iron atom to a peptide

Hi All,

This is my first post to the form. I'm a new user to Rosetta.

I am using the ligand_docking application to dock an Fe(III) atom to a protein structure, and am running into difficulty. A few questions:

1. Is ligand_docking appropriate for docking a single atom to a protein molecule?

2. If ligand_docking is appropriate, what is the best way to do it? When I try to use the 1_setup.sh script produced by arls.py to set up a ligand docking run, it complains that I need to have at least 3 atoms in the Mol2 file used to define the ligand (the Fe atom).

Post Situation: 

Relax protocoll short pdb of AAA petide

I have used Modeller to to produce linear peptide. When I refine the linear peptide using relax protocol an peptide with for instance AAA is shorted to AA. How do I prevent this from happening. I am using relax.linuxgccrelease -database /home/knut/rosetta/rosetta_database -in:file:native $f -out:prefix relaxed_ -out:nstruct 1 this command with these options.

Knut J

Post Situation: 

is the RosettaNMR protocol available in Rosetta 3.x?

Hi all users of Rosetta,
I am a yung PhD student and is first time approach to Rosetta. I need to use RosettaNMR for my research program to include NOE RDC PCS in Rosetta calculation. But I noted that RosettaNMR is available only on Rosetta 2.x. Hence I ask you if in Rosetta 3.x is also possible include RDC data, because I found only c++ class to manage NOE and dihedral data.

Thanks.

Best regard.

Post Situation: 

Using rosetta 3 to make a fragment library and then use it to model loop of a protein structure

Hi,

I want to know how to generate a fragment library for rosetta ... The method given in the documentation is not the one I want as , I want to retreive fragments of 8 or above residues taken from pdb consisting the loop regions of various proteins not on the basis of any resembling sequence.. Also I want to know what's the structure of this file consisting the fragments (means what does the last 4 columns tell)

1bvy F 24 L E -111.045 104.882 178.947 0.947 12.265 16.922 3 0.000 P 1 F 1

Post Situation: 

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