# Unsolved

The problem hasn't been solved

## READ THIS BEFORE YOU POST

- 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:

## Confusion for Input Tutorial

Category:
Compilation

Hi All,

\$ ./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:

Post Situation:

## Ddg calculation for a metalloprotein using APBS

Category:
Scoring

Hi all,

I am trying to calculate Ddg for a protein complex, which is made of 3 chains: A, B and C.

The chains B and C have a zinc-finger each, which are a zinc ion complexed by four CYS side-chains.

To calculate the Ddg I am using the SetupPoissonBoltzmannPotential mover followed by the Ddg filter, in order to separate chain B from chain A+C and calculate the binding energy.

Post Situation:

## Is cis-Glycine okay?

Category:
Loop Modeling

Yes, that is not a typo for cis-proline! I don't have an issue just curious. I have a loop that Rosetta Remodel (all PIKAA entries) is struggling with despite the generic_aa set to G (but most likely for biological reasons), which got me thinking...

Post Situation:

## Linear peptide versus cyclic peptide binding prediction

Category:
Design

I have used ROSIE server to analyze protein-antibody interaction and predict peptide sequences of antibody that would interact with the protein.

The analysis revealed 3 hotspots of the antibody sequence as in the picture attached. It did make sense to me that the predicted linaer peptides from antibody sequence were chosen from 1st and 3rd hotspots from the figure with highest contact points with the protein.

Post Situation:

## ./scons.py error in building

Category:
Compilation

I am in the stage of trying to install and build rosetta and I have reached the point where I am using scons.py.

I have been following the guide (https://www.rosettacommons.org/demos/latest/tutorials/install_build/install_build) so far, but I reach a road block when I build with scons.py. my commands and the results are as follows:

Post Situation:

## Rosetta Remodel - Error in core::conformation::Conformation::residue(): The sequence position requested was 0.

Category:
Design

Dear caretakers/kind strangers,

I ran into an error that i do not understand when trying to do de-novo modelling of a helix linker using REMODEL. When i leave the blueprint file without any new residues it runs fine. But when i add new residues at the end (C Terminal) the program recognizes it is a C terminal extension, but throws this error.

Post Situation:

## Cluster Compile Error: g++ ---no-as-needed

Category:
Compilation

Hi,

I'm trying to install Rosetta 2019.22 in my Home directory of a cluster (which I have done successfully on a different cluster in the past).

However, I'm getting an error:

-------------------------------------------------------------------

Post Situation:

## Linux Ubuntu build is missing Dynamically Linked Libraries (fail during unit test)

Category:
Compilation

Hello,

I've installed Rosetta 3.11 for Linux ubuntu 16.04 without any failure.

However, I encountered some missing binaries after running unit tests. This is the general command I use for the unit test.

python scons.py -j #numproc mode=debug cat=test

The snippet below is the output returned from the unit test.

Post Situation:

## Symmetry mode in Remodel for N-terminal extension

Category:
Design
Loop Modeling
Symmetry

Hello,

I am trying to use Remodel for N-terminal extension of my homotetramer. I am passing in a single subunit (chain A) and symmetry file (4 subunits identified) with my blueprint with the extra residues of interest. I am getting the following error:

File: src/protocols/loops/loops_main.cc:253
[ ERROR ] UtilityExitException
ERROR: Can't build a fold tree from a loop with an unspecified cut point.

Post Situation: