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cutpoint error!

Submitted by monos_morpheus on Thu, 2011-04-07 08:04

Hi, I'm trying to use docking_protocol.linuxgccrelease on a pdb structure where it is made up of 2 chains, one is the actual protein, while the other is a peptide of small length.

When I ran that module, I got the error:

ERROR: cutpoint
ERROR:: Exit from: src/protocols/docking/util.cc line: 91

What is this cutpoint error about and how can I go about solving it.? Please advise. Thanks. =)

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Rosetta 3 - General

CentOS-5 x86_64 python 2.6.6 (self compiled --enable-unicode=ucs4 --enable-shared --enable-threads) issue with 1.1/2.0

Submitted by tru on Wed, 2011-04-06 11:34

I installed both:
PyRosetta-Release1.1-r34968.linux.64Bit.tar.bz2
PyRosetta.ScientificLinux-r40608.linux.64Bit.tar.bz2

PyRosetta-Release1.1-r34968:

[tru@mestizo ~]$ iPyRosetta
/c5/shared/pyrosetta/PyRosetta-Release1.1-r34968.linux.64Bit/IPython/Magic.py:38: DeprecationWarning: the sets module is deprecated
from sets import Set
Python 2.6.6 (r266:84292, Apr 6 2011, 19:50:10)
Type "copyright", "credits" or "license" for more information.

IPython 0.9.1 -- An enhanced Interactive Python.
? -> Introduction and overview of IPython's features.

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PyRosetta - Build/Install

Rosetta 3.2.1 CentOS-5 x86_64 gcc: "scons cat=test mode=release" failure

Submitted by tru on Wed, 2011-04-06 08:01

python 2.4
scons 2.0.1
gcc 4.1.2 (CentOS-5 version)


[tru@liberte rosetta_source]$ scons -j8 bin mode=release
...

finished fine ...

but testing fails:

[tru@liberte rosetta_source]$ scons -j8 cat=test mode=release
scons: Reading SConscript files ...
svn: '.' is not a working copy

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File "/c5/shared/rosetta/3.2.1/rosetta_source/SConscript", line 40, in ?

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.

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Rosetta 3 - Build/Install

How to set up options in rosetta

Submitted by alejandro on Wed, 2011-04-06 02:08

Good morning,

I'm quite new to Rosetta software and I'm developing an application that uses Rosetta features. My application works fine but I'm quite annoyed with the output of Rosetta. Is there a way to set verbosity level in the shell to 0? I guess this feature exists but I've been unable to make it work so far. I tried

core::options::option.add_relevant(core::options::OptionKeys::run::silent);

but this doesn't seem to have effect.

Can anyone point me to the right direction?

Thanks a lot
Alejandro

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Rosetta 3 - General

How to set up Rosetta 3 in Mac OS

Submitted by hourosetta on Tue, 2011-04-05 20:17

Hi,

I am brand new for Rosetta. I am planing to do homology modeling, protein-protein docking, and small molecule docking with Rosetta. I bought a MacBook Pro for these purposes, after consulting a few people in this field. I downloaded the most recent version of Rosetta, but I don't know how to have Rosetta to run in my Mac. Your help will be greatly appreicated.

Zhanjun

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Rosetta 3 - Build/Install

RosettaAntibody

Submitted by mpendleton on Mon, 2011-04-04 10:27

I have been using Rosetta for about a year now and have been interested in using RosettaAntibody for some time now. I have held off installing Rosetta++ in the hopes that RosettaAntibody would be included in the new 3.2 build. Does anyone know if this is the case, or will I still need to install Rosetta++ in order to access that algorithm without taking up space on the RosettaAntibody webserver?

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Rosetta 3 - Applications

loop model error

Submitted by albumns on Sun, 2011-04-03 00:26

Dear:
I am trying to run the loop model protocol by the command: loopmodel.linuxgccrelease @kic.options

However, it doesn't work, and here is my log file. I would be very appreciated if you can give me some advices.

By the way, does the loop protocol support MPI?

Thank you very much

-------------------------------log-----------------------------------------------
core.init: Mini-Rosetta version exported from unknown
core.init: command: loopmodel.linuxgccrelease @kic.options

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Rosetta 3 - General

How do I add hydrogen atoms to my PDB file?

Submitted by monos_morpheus on Wed, 2011-03-30 03:30

I'm currently using Rosetta 3.2.1, and I wish to add missing H atoms to my PDB file. I know that in the past, a clean_pdb.py script was created by the Meiler Lab to help with such a problem. However, I'm unable to locate this file anywhere in Rosetta 3.2.1. Is there any ways to locate this file or is there other scripts made to satisfy such a problem.?

Thanks.

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