The problem hasn't been solved
Hello,
I'm using ubuntu 10.10, scons 2.0, python 2.6.6 and gcc 4.4.5
I built a release version of Rosetta, here are the last few lines of the building process
sh: o: not found
Install file: "build/src/release/linux/2.6/32/x86/gcc/rna_extract.linuxgccrelease" as "bin/rna_extract.linuxgccrelease"
(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 *
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
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 ...
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
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
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)
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).
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
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.