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Need help with compilation (How to test if compilation is sucessful)

Submitted by greenfur on Fri, 2012-06-29 12:29

I logged in as a regular user without superuser privilege.
After I downloaded rosetta 3.4, and unzipped the file "rosetta3.4_bundles.tgz", I unzipped all the .tgz files in the directory "rosetta3.4". In the sub-directory "rosetta_source", I typed "python external/scons-local/scons.py bin mode=release". After some time (hours), the compilation seems completed. then in the directory rosetta3.4/rosetta_source/bin, I typed "minirosetta.linuxgccrelease", get the following error message:

core.init: Mini-Rosetta version unknown from unknown
core.init: command: minirosetta.linuxgccrelease

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Rosetta 3 - General

"No SConstruct file found" when install rosetta 3.4 on ubuntu 11.10

Submitted by lchen on Fri, 2012-06-29 10:45

According to the instruction, I first installed scons and tested it, it seems working:

*********************
~/scons-2.1.0$ scons --version
SCons by Steven Knight et al.:
script: v2.1.0.r5357[MODIFIED], 2011/09/09 21:31:03, by bdeegan
on ubuntu
engine: v2.1.0.r5357[MODIFIED], 2011/09/09 21:31:03, by bdeegan
on ubuntu
engine path: ['/usr/local/lib/scons-2.1.0/SCons']
Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009,
2010,
2011 The SCons Foundation
**************************

Then I run Resetta installation and get error below:

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Rosetta 3 - Build/Install

The design of a helical peptide

Submitted by Jacob-kong on Tue, 2012-06-26 06:26

Dear Rosetta developers,

I am interested in the de novol design of a peptide with helical conformation which could bind a specific protein partner with enhanced affinity. However, when consulting the user guide, i lost my way about the specific method. So could you be so kindly to tell me which method or module in Rosetta can do such kind of case , or provide me a step-by-step guidance.

What i intended to do was listed in the following:

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Rosetta 3 - General

spline constraint

Submitted by jadolfbr on Mon, 2012-06-25 04:43

I havn't been able to find an example of the spline constraint histogram format...is there an example somewhere that I missed?

Also, within the constraint code, is it possible to give an already-generated spline to use for the constraint? What are the requirements of the spline (bicubic, tricubic, etc)?

-Jared

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Rosetta 3 - General

How to do the testing job for Rosetta 3.4 ?

Submitted by Jacob-kong on Sun, 2012-06-24 19:43

Hi everyone,

I am trying to install Rosetta 3.4 on CentOS release 5.5. I built the Rosetta executables with the command "scons bin mode=release" according to the user guide . However, i lost my head for how to do the testing jobs. I searched through the forum and it seems that i should do the unit test firstly and then try the integration test. So my first questions is whether this testing routing make sense.

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Rosetta 3 - Build/Install

postive score models from AbinitioRelax

Submitted by xpzhang on Fri, 2012-06-22 12:34

I am trying to fold a protein of 140 AA in Rosetta 3.4 AbinitioRelax with the flags suggested in Rosetta 3.4 manual page:
http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/d0/d...

-in:file:fasta ./t000_.fasta
-in:file:frag3 ./aat000_03_05.200_v1_3
-in:file:frag9 ./aat000_09_05.200_v1_3
-database /home/zhang/local_programs/rosetta3.4/rosetta_database/
-jran 1234567
-abinitio:relax
-nstruct 10
-out:pdb
-use_filters true
-psipred_ss2 ./t000_.psipred_ss2
# -kill_hairpins ./t000_.psipred_ss2
-abinitio::increase_cycles 10
-abinitio::rg_reweight 0.5

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Rosetta 3 - General

Dock antibody at the epitope of antigen

Submitted by styang on Fri, 2012-06-22 05:44

Deal all:

I am a beginner of computational protein docking. For my current project, I am going to dock Ab at Ag using PyRosseta.
Is there any option or parameters that I can constrain the region (epitope) of Ag to be docked by Ab? I would like to extract the value of scoring function based on this constrain (epitope).

Please having your comments or suggestions regarding how to do that.
Thanks so much,

Hsih-Te

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