Building source/bin
Submitted by spage789 on Thu, 2014-06-26 10:26
You are here
Solved
The problem has been solved
What build to download?
Submitted by ajasja on Wed, 2014-06-18 09:10
Category:
PyRosetta
In the list of full releases there are a number of newer files than what is listed on the pyrosseta.org/dow.
Are these also stable releases? What does the monolith mode mean? (as in mode=release.branch=release.monolith.html) And what is the namespace mode?
Thank you for satisying my curiosity,
Ajasja Ljubetič
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Error when running prepack of PLEXPEPDOCKING
Submitted by phanvy on Wed, 2014-06-18 07:11
Category:
Docking
Hello everyone!
I use Plexpepdocking (Rosetta 3.4), in my structure have one ion Zn , but Plexpepdock can not recognize it.
Please take a look on my pdb file and tell me how to fix this Error.
Thank you so much for your help.
Thank!!!
this is the flag for pre_packing
-s tryzn.pdb
-database /home/tuongvy/SW/rosetta3.4/rosetta_database
-flexpep_prepack
-ex1
-ex2aro
This is the ERROR
ERROR: unknown atom_name: ZN CA
ERROR:: Exit from: src/core/chemical/ResidueType.cc line: 1692
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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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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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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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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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Computing pairwise energies for rotamers
Submitted by pachecoj on Sat, 2014-05-03 17:52
Category:
Structure prediction
I am writing an application for sidechain packing and am trying to figure out how to compute the energy table for all pairs of rotamers on a given edge.
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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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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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