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"Local sequence-structure compatability" in "design of ideal protein structures"

Submitted by petrikigor on Sun, 2012-12-02 09:25

I'm not sure if this the best place to ask, but I couldn't think of anywhere better:

I read and was really impressed by the conclusions of Koga, et al. "Principles for designing ideal protein structures". One thing that really intrigued me was the step in the process described as filtering for "local sequence structure comparability". Neither the article nor the example code seem to indicate how this filtering was done. The example RosettaScripts code simply indicates
## The filter for local sequence structure compatibility was done without using RosettaScripts

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Rosetta 3 - General

pNNMAKE compilation

Submitted by adva on Sun, 2012-12-02 03:59

Hello,
I'm trying to make fragments using rosetta 3.2 in order to run membrane ab initio protocol.
after trying to create pNNMAKE.gnu using "make" command I got this error:

----------------------------------------------------------------------
SYSTEM SETUP [make.system]
COMPILER=gnu @ adva
F77=g77
FFLAGS=-finline-functions -funroll-loops -W -ffixed-line-length-132 -Wimplicit -O -ffast-math -malign-double
FOPTIMFLAGS=-O -ffast-math -malign-double
FDEBUGFLAGS=-g -Wall -Wimplicit -Wsurprising -Wformat -W
FPROFILEFLAGS=-pg
LINKFLAGS=

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Rosetta 3 - General

fa_plane enregy term in scoring weights

Submitted by ytao on Fri, 2012-11-30 20:25

Hi,

I'm working on a protein that appears to have some aromatic groups stacking in the x-ray structure, but I could not see such conformers in my models(Ca RMSD 1.1 A to X-ray structure) built with rosetta.
I found there is this term "fa_plane" in the scoring weights that is supposed to describe "pi-pi interaction between aromatic groups, by default = 0", however, there's no scoring method defined for it in the source code. So if I change the weight of this term, it will only give an error message: "ERROR: Requested ScoreType fa_plane does not have a registered EnergyMethodCreator."

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Rosetta 3 - Applications

How to use -cst_fa_file and -relax:constrain_relax_to_native_coords at the same time

Submitted by Anatol on Thu, 2012-11-29 14:12

Hi:

I would like to relax my X1.pdb structure with the atom coordinate constraints relative to the backbone atoms of another structure X2.pdb and some other constraints given in -cst_fa_file constrains.
Here is what I have done:

relax.linuxgccrelease -database /home2/ruvinsky/simcode/rosetta_database -in:file:s X1.pdb -in:file:fullatom -out:file:fullatom -relax:fast -score:weights score12_full -out:pdb -ex1aro -ex1 -ex2 -out:nstruct 10 -relax:constrain_relax_to_native_coords -in:file:native X2.pdb -cst_fa_file constraints

It failed with the following error message:

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Rosetta 3 - Applications

too many constraints result in no output pose

Submitted by Yao Wu on Sun, 2012-11-18 23:45

Hi,everyone.
When I applied 11 distance constraints, get from chemical cross-linking assay, into Protein-Protein docking, there is no output pose and also no error reported.
Here is the output log:
"""
protocols.jd2.JobDistributor: poseinp_0001 reported failure and will retry
... ...
protocols.jd2.JobDistributor: poseinp_0012 reported failure and will retry
"""

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Rosetta 3 - Applications

Missing movers in OSX PyRosetta

Submitted by lah435 on Fri, 2012-11-16 15:45

The RigidBodyMovers are missing in the OSX build of PyRosetta. Examples: On Ubuntu: In [3]: help(RigidBody RigidBodyDofPerturbMover       RigidBodyMover RigidBodyDofRandomizeMover     RigidBodyPerturbMover RigidBodyDofRandomTransMover   RigidBodyPerturbMover RigidBodyDofSeqPerturbMover    RigidBodyRandomizeMover RigidBodyDofSeqRandomizeMover  RigidBodySpinMover RigidBodyDofSeqTransMover      RigidBodyTransMover RigidBodyDofTransMover

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PyRosetta - General

Homodimer interface design

Submitted by petrikigor on Fri, 2012-11-16 10:57

Hi,

I am trying to use RosettaDesign or (preferably) enzdes to redesign a defined interface. I would like the interface to be homodimeric. Can symmetry be invoked in enzdes or RosettaDesign to ensure that both monomers are mutated simultaneously? If so, is there a guide to this?

Thanks,
- Igor

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Rosetta 3 - Applications

error with profit

Submitted by jchin on Thu, 2012-11-15 10:00

Hi,

I get an error below with profit being called on profit.in

Scan one or more sequences with a simple frequency matrix
Profile or weight matrix file: Error: Unable to open file 'QUIET' for input
Profile or weight matrix file: Error: Unable to open file 'ZONE CLEAR' for input
Died: profit terminated: Bad value for '-infile' and no more retries
256 at /home/.../immunity/antibody/scripts/ram_buildloop_wrapper4.pl line 12

__

The contents of profit.in (below), don't seem to match the expected input for profit.

QUIET
ZONE CLEAR
ATOMS CA
templatelightheavy.pdb queryL.pdb

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Rosetta++ - Build/Install

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