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I'm a total beginner to Rosetta 3.2 and there are no tutorials for me to follow. Can someone help.? =)

Hi, I'm currently an undergraduate research student in Singapore. My prof has just tasked me to try out Rosetta for docking. However, he is also new to the program, and so we are sort of stuck on how to start even a basic docking. We are using SUSE Linux. We hope that someone would be kind enough to get us started on a very basic tutorial on docking like the commands used, before we proceed on to explore the features further.

Thanks. =)

Post Situation: 

Excessive disk use in Rosetta download and build processes

The software I build and install gets pushed to standalone installations on about 100 different machines, and the installation usually lives on higher-cost storage (i.e. RAID or a SAN, etc), and then all those installations are backed up somewhere or other, so I usually take the time to weed out as many unnecessary files as possible. It makes everyone's life a little better.

Looking at the Rosetta packaging, there are a number of opportunities for improvements. The first one is very easy. Here's an expanded rosetta3.2_bundles.tgz:

$ du -k --max-depth=1 | sort -n
48 ./.svn

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Error during installation of rosetta2.3 in Blue gene

Hi

I am trying to install rosetta2.3 in IBM Blue gene
Compiler: xlc++
Mpi : mpixlC

The error got during compilation:
mpixlC -c -I. -Isrc -Iexternal/include -Isrc/platform/linux/ -O3 -qhot=nosimd -DNDEBUG -DUSEMPI -qarch=440 -qtune=440 -qmaxmem=-1 -qlanglvl=c99__func__ -MT.xlc++_ppc.map_sequence.d -MF.xlc++_ppc.map_sequence.d map_sequence.cc -o .xlc++_ppc.map_sequence.o
"src/ObjexxFCL/FArray1DB.hh", line 477.29: 1540-0274 (S) The name lookup for "equal_dimensions" did not find a declaration.

Post Situation: 

Build Error, ubuntu 10.10, scons 2.0, python 2.6.6 and gcc 4.4.5, truncation

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"

Post Situation: 

(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: 

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