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A question about Multiple constraints

Submitted by kxiao on Mon, 2014-06-16 07:02
Category: 
Constraints

Hi, all.
I've got a question about the Multiple Constraints, is there any differences between multiple-line constraints inside and outside a MultiConstraint block?
For example, if I want to apply two constraints, CST1 and CST2, what is the difference between the following two constraint files?

file1:
MultiConstraint
CST1
CST2
END

file2: (with out MultiConstraint block)
CST1
CST2

I am not sure if they are the same.

Anyone can help me? Thanks a lot in advance.

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Rosetta 3 - General

Architecture Problem

Submitted by jzabilansky on Wed, 2014-06-04 13:30
Category: 
PyRosetta

Hello,

I am currently trying to work with PyRosetta on my system:

Mac OS X 10.9.1 64 Bit

with Python 2.7.6 64 Bit

I've downloaded PyRosetta.MacOSX.Lion-r55641.64Bit and after decompressing the file, setting the PyRosetta Environment and opening Python, I run import rosetta and get the following error.

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PyRosetta - Build/Install

ddg_monomer and membrane proteins

Submitted by afmo on Tue, 2014-05-20 02:37
Category: 
Scoring
Membrane

Dear all,
I am a new Rosetta (3.5) user and I would like to study the effects of some point mutations on a monomeric transmembrane protein.

Can ddg_monomer properly predict the change in stability induced by point mutations in transmembrane proteins? If yes, should I specify a particular score function file using -ddg:minimization_scorefunction option? I would like to study mutations in both, the transmembrane (membrane-facing and not) and the extracellular region of the protein, should I treat them separately?

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Rosetta 3 - Applications

Ligand Docking Protocol now available for academic users

Submitted by Sergey on Sat, 2014-05-10 14:39
Category: 
ROSIE

Hi Everyone,

Our ROSIE Server now have Ligand Docking Protocol (developed in Meiler Lab at http://www.meilerlab.org ) open for academic users. Please visit http://rosie.graylab.jhu.edu/ligand_docking for documentation and job submission.

Best,

Sergey.

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ROSIE - General

Binary silent Output file reading problem

Submitted by wlzhang on Sun, 2014-04-20 17:47

Hi,all:

I have run an ab initio relax with binary silent output and encountered a reading problem from the outputfile.

The input looks like:
/rosetta_source/bin/AbinitioRelax.linuxiccrelease @flag

The flags are
-database /rosettatorun/rosetta_database
-in:file:fasta sec2.fasta
-in:file:frag3 ../../aat000_03_05.200_v1_3
-in:file:frag9 ../../aat000_09_05.200_v1_3
-abinitio:relax -relax:fast
-abinitio:increase_cycles 10
-abinitio::rg_reweight 0.5
-abinitio::rsd_wt_helix 0.5
-abinitio::rsd_wt_loop 0.5
-use_filters true
-psipred_ss2 ../../sec2.psipass2

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Rosetta 3 - General

Cluster application, How does it sort decoys by energy?

Submitted by Apiwat on Wed, 2014-04-16 01:52

Hello all,

I have clustered 1,000 decoys by using cluster application in Rosetta with flags below.

cluster.linuxgccrelease

Flags
-l list_cut_off_decoy
-cluster:radius 3.0
-in:file:fullatom
-score:weights score12
-score:patch docking
-cluster:sort_groups_by_energy
-database ~/database

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Rosetta 3 - General

score_jd2.mpi.linuxgccrelease failed

Submitted by fred on Wed, 2014-03-26 13:54

Hi there,
I was trying to score 100k decoys in a silent file using the Rosetta's score_jd2.mpi.linuxgccrelease with the command line:
> score_jd2.mpi.linuxgccrelease -in:file:fullatom -in:file:silent query_silent.out -out:file:silent_struct_type binary -out:file:silent scored_silent.out

I've got the following on screen:

...
core.pack.dunbrack: (12) Reading /cluster/apps/fred/rosetta_2014wk05/main/database/rotamer/ExtendedOpt1-5/asp.bbdep.rotamers.lib
core.pack.dunbrack: (12) Reading /cluster/apps/fred/rosetta_2014wk05/main/database/rotamer/ExtendedOpt1-5/asp.bbdep.densities.lib

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Rosetta 3 - Applications

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