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Relaxation vs minimisation

Submitted by mm on Fri, 2020-03-13 04:49
Category: 
Structure prediction
Scoring
PyRosetta

Hi all,

I am very new to the computational structural biology community and I have tried to model a structure by using a software which runs MODELLER on the background. However, my result shows a number of steric clashes and a very high fa_rep when I calculate it with PyRosetta. I am therefore trying to improve the structure before moving on with the rest of my analysis. 

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PyRosetta - Applications

antibody_numbering_converter cannot recognize the IMGT scheme

Submitted by cryosky on Sat, 2020-02-29 23:12
Category: 
Docking

To whom it may concern:

Hi I want to convert my antibody structure from Chothia to IMGT. I use the following command and get an error "ERROR: Illegal value specified for option -antibody:output_ab_scheme : IMGT". I am wondering is the IMGT scheme already cancelled in the number converter program? This is a 2019.35.60890 version.

/home/rosetta_bin_linux_2019.35.60890_bundle/main/source/bin/antibody_numbering_converter.linuxgccrelease -input_ab_scheme Chothia -output_ab_scheme IMGT -s 1ahw_chothia.pdb

 

Best regards,

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Rosetta 3 - Applications

MotifGraft error: "Residue connection id changed when creating a new residue at seqpos"

Submitted by dfcoelho on Mon, 2020-02-03 11:09
Category: 
Design

Hello everyone,

I am trying to use MotifGraft mover to graft an epitope to a scaffold protein (actually there is a structure library, parsed with -l list).

The xml script is attached.

My command line is as follow (I am first trying a very loose boundary conditions, I'm aware about the higher RMSD/atom_clash values):

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Rosetta 3 - General

Distorted metal coordination geometry after relaxation (SetupMetalMover was used, fold tree and constraints were set manually)

Submitted by TLP on Tue, 2020-01-21 11:18
Category: 
Design
Scoring
Constraints
PyRosetta

 

Hello,

I am trying to relax Zn containing peptides like zinc fingers, but always got distorted geometries of the coordination site and much higher scores after the relax. Still, the rest of the peptide looks nice.

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PyRosetta - Applications

Centroid mode minimization

Submitted by Martin Floor on Tue, 2020-01-21 07:34
Category: 
Structure prediction

Hi everyone,

I was wondering if there is something like the Relax Application but to use it directly in centroid mode. I know AbInitio uses fragment insertion to start building structures in centroid mode that are later fed to the All-Atom relax application, but is there something that can do a montecarlo local exploration without leaving centroid representation?

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Rosetta 3 - Applications

Rosetta Antibody: Unable to open file and terminates

Submitted by denatured on Thu, 2019-12-12 11:26
Category: 
Compilation

Hello, please note I'm revising my posting with some major updates, apologies to the 9 viewers who have come here prior as this will read completely different.

 

I'm encountering a read error with antibody_H3. Below is the executable I ran (I've also reproduced the error with .static mode): 

mpiexec -np 4 $ROSETTA3/bin/antibody_H3.cxx11threadmpiserialization.linuxgccrelease \
  @abH3.flags

abH3.flags looks just like:

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Rosetta 3 - General

PyRosetta on Ubuntu 16.04 build error

Submitted by denatured on Fri, 2019-11-29 10:23
Category: 
Compilation

- OS type/version/arch:
Linux Ubuntu 16.04  (on an Azure virtual machine)
- Python version:
3.5

- Version of PyRosetta including SVN revision number.
PyRosetta4.Release.python35.ubuntu.release-236.tar.bz2

- Version of Rosetta:
Rosetta 3.11 for Linux

 

Hello, I've installed PyRosetta and upon importing in Python3.5 I receive the following error:

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PyRosetta - Build/Install

Confusion for Input Tutorial

Submitted by mcguirst on Wed, 2019-11-20 12:29
Category: 
Compilation

Hi All,

I have downloaded Rosetta 3.11 and built it with Scons.py using 

$ ./scons.py -j 4 mode=release bin 

The building of the binaries seems to work correctly providing me with:

scons: done building targets.

 

I am now attempting to familiarize myself with Rosetta by traversing the tutorials starting with the Input & Output Tutorial so I am within this directory:

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Rosetta 3 - Build/Install

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