# Unsolved

The problem hasn't been solved

## READ THIS BEFORE YOU POST

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

- Version of PyRosetta including SVN revision number.

Thank you!

Post Situation:

## Secondary Structure Relax

Category:
Design

Hello everyone,

I have generated a protein, and as you can see it seems to have almost a good backbone structure (the helices and the sheets are clearly visible but not quite there). Attached are two photos, Figure 1 is what I have generated, Figure 2 is the original crystal structure.

Is there a way to relax the structure as to emphasise for the secondary structures. In other words, push the structure to form secondary structures? or complete the hydrogen bonds for secondary structures?

Post Situation:

## PyRosetta compiled with GLIBC 2.12

Category:
Compilation
PyRosetta

Hello,

We are trying to install PyRosetta on CentOS 6.  The current compilation of PyRosetta (PyRosetta4.Release.python27.linux.release-171.tar.bz2) requires GLIBC_2.14.

However, our system's GLIBC version is 2.12 and the compilation of PyRosetta stop with the error

ImportError: /lib64/libc.so.6: version GLIBC_2.14' not found (required by /cm/shared/apps/pyrosetta/python/2.7/4.171/lib/python2.7/site-packages/pyrosetta-2018.9+release.333d996-py2.7-linux-x86_64.egg/pyrosetta/rosetta.so)

Post Situation:

## Running a ReportFSC mover between two .mrc maps

Category:
Structure prediction

I'm trying to run a ReportFSC mover between two maps to debug some issue in my structure refinement protocol (https://www.rosettacommons.org/node/10195). I'm fairly new to Rosetta scripting, below you can find my attempt. What am I doing wrong? Thanks in advance.

Post Situation:

## Sample dihedral database

Category:
PyRosetta

Good morning,

I have a database of dihedral angles in this order: residue psi psi. Is is possible to use pyrosetta to sample randomly throuh this database,

applying random psi and psi angles to a pdb pose, using a movemap? Imagine that my sequence is AQAAVFGT; so the script would retrieve randomly from the database the dihedrals corresponding to residues in the sequence and output a pose.

is this possible? Maybe with a loop with the SetTorsion mover?

Thank you,

cheers

Post Situation:

## Rosetta matching error

Category:
Enzyme Design

I am working on ligand-based protein design by rosetta. I am getting a constant error on the rosetta matching algorithm to find possible binding sites in the protein molecule for the desired ligand. The error that I receive is "Cannot normalize xyzVector of length() zero". I tried running the script on different servers and multiple times but I get the same error everytime. What could possibly be going wrong?

Post Situation:

## ddg_monomer consumes massive RAM

Category:
Design

I am trying to run the ddg_monomer high-res protocol on a protein. I am running this on a Linux system with 4 GB of RAM. Immediately after the protocol begins to run, RAM usage gets very high and my computer freezes. It remains frozen indefinetely. Is this normal? Usually when I run other ROSETTA protocols, the computer is perfectly usable with the job running in the background.

I am using all the default settings from the high-res protocol (row 16 of Kellogg et al) from the documentation:

Post Situation:

## ΔΔG Calculation of a Mutation with PyRosetta

Category:
Scoring

Hi everyone,

We are trying to replicate the experiment by Alford et al. (2017) in our lab to calculate the ΔΔG of T193V mutation for the RT-RH-derived peptide bound to HIV-1 protease (PDB entry 1kjg). However, we have been getting values that are different from the reported ΔΔG of –4.95 kcal/mol and it’s likely due to errors in our code.

Post Situation:

## Structure refinement guided by Cryo-EM density maps

Category:
Structure prediction

I have a few questions regarding this tutorial here:

https://www.rosettacommons.org/demos/latest/public/electron_density_structure_refinement/structure_refinement`

1) What does ReportFSC do exactly? Does it generate a density map from the atomic model and correlates it to the test map?

Post Situation:

## demos/public/ideal_proteins Segmentation fault

Category:
Design

Dear All,

I am using rosetta_bin_linux_2017.52.59948_bundle to run demos/public/ideal_proteins. The running command is

"rosetta_scripts.static.linuxgccrelease -s input.pdb -parser:protocol input.xml -nstruct 10 -restore_talaris_behavior".

Since I got

"

score_typeextract failed: fa_plane

ERROR: bad line in file myweight.wts:fa_plane 0

ERROR:: Exit from: src/core/scoring/ScoreFunction.cc line: 453

Post Situation: