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When posting build/install question please specify the following information about your system and PyRosetta version, this will allow us to answer your questions more accurate and faster:

- OS type,
- OS version
- OS arch (32 or 64bit)
for example: Ubuntu Linux 10.04 32Bit or Mac OS X 10.6

- Python version
- Python arch (32 or 64bit) if different from OS

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Thank you!

Post Situation: 

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

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.

Post Situation: 

Rosetta Resfile header

Category: 
Design

I have been using Rosetta design for quite a while but I did not pay attention to what Resfile header would do. I looked for descriptions and examples files different people have shared and used and I am unable to understand when I should specify NATRO or NATAA in the header?

I want to perform different tasks. For example:

1) Mutate specific residue to ALLAA and I use header like:

NATRO
start
30 H ALLAA

whereas, I found someone using following header:

Post Situation: 

Working through tutorials: expected output scorces differ from calculated results

Category: 
Scoring

Hi,

I'm new to Rosetta and currently working through the tutorials.

I often recognized that  the the score values produced by the recent version "Rosetta 2019.47" on my computer differ from the ones cited in the tutorials and given expected_output.

e.g.:

in the Scoring Tutorial  (subchapter "Changing the Score Function") the command

ROSETTA3/bin/score_jd2.linuxgccrelease @flag_docking

with flags

Post Situation: 

Error during single state design

Category: 
Design

Hi,

During single state design of protein the following error is encountered after relaxing the structure at the fixed backbone design stage  and also by design iterated by backrub motion.

protocols.jd2.JobDistributor: [ ERROR ]

[ERROR] Exception caught by JobDistributor for job 4MUI_relax_design_0010

Post Situation: 

How to freeze ligand during FastRelax?

Category: 
Small Molecules

I want to fix (freeze) ligand during fastrelax because the fastrelax changes ligand conformation weirdly .

This happens even with params file of the ligand.

Therefore, I tried ignore_unrecognized_res, but this option just not outputting the ligand in the result file.

Here I attach screenshots.

 

Thank you

Post Situation: 

Error of compiling AbrelaxApplication.cc

Category: 
Structure prediction

Hi,I want to use ResolutionSwitcher in Montecarlo.cc to relax pdb after stage1-4,when i add "#include<protocols/abinitio/ResolutionSwitcher.hh> in MonteCarlo.cc",it turn to be a error"Resolution switcher was not declared in this scope".

I included all the header files but still not working.

Post Situation: 

What is the best protocol to predict the missing residues in X-ray crystallisation?

Category: 
Structure prediction

I know the full amino acid sequence for my protein. I have obtained its X-ray crystal PDB structure, as well as the mtz file from the crystallisation. There are several loops and termini not resolved. Can I ask what is the best protocol to predict the missing part? I understand it would still not be fully "true" after Rosetta's modelling. I just want to have a "mostly likely" one that can be used as the starting point for my molecular dynamic simulation.

Post Situation: 

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