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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

- Version of PyRosetta including SVN revision number.

Thank you!

Post Situation: 

Error msg while compiling on a new cluster

Category: 
Compilation

Not sure why scons is failing on a new cluster

>./scons.py bin -j16 mode=release extras=mpi

I see en error:

scons: *** Do not know how to make File target `bin' (/usr/projects/xyz/shared/rosetta_3.10_release/main/source/bin). Stop.

rosetta_3.10_release could be easily compiled on my local machine.

Post Situation: 

Error with etable_atom_pair_energies()

Category: 
Scoring

I am new to Pyrosetta and programing and I am learning how to use Pyrosetta. So when I was practicing scoring with Workshop #3 bullet point 5, I came across a error, and I have no idea what's wrong with.

Here is what I did. 

r1 = pose.residue(24)

r2 = pose.residue(20)

a1 = r1.atom("N")

a2 = r1.atom("O")

etable_atom_pair_energies(a1, a2, scorefxn)

Post Situation: 

Rosetta_CM error unrecognized atom 'CS' this atom is not in PDB

Category: 
Structure prediction

Hi all,

 

       I'm sorry if this is an old thread, I did find other forums dealing with unrecognized atoms but in those threads my problem was not resolved.  I am trying to follow the rosetta_CM tutorial and I got through the setup_rosetta_CM.py script and it generated the .xml file which I checked and it looked good. However, when I run the hybridized steps using rosetta scripts I get this error:

 

ERROR: unrecognized atom_type_name 'CS'

Post Situation: 

Rosetta3.10 on macOS segmentation fault 11

Category: 
Structure prediction

 

I have tried several times to install Rosetta3.10 for macOS version 10.14.2. My system info is:

Model Name: MacBook Pro

  Model Identifier: MacBookPro15,2

  Processor Name: Intel Core i7

  Processor Speed: 2,7 GHz

  Number of Processors: 1

  Total Number of Cores: 4

  L2 Cache (per Core): 256 KB

  L3 Cache: 8 MB

  Memory: 8 GB

Post Situation: 

RosettaMP: issue with generating .lips4 file

Category: 
Structure prediction

Hi Rosetta users,

I am experiencing trouble using RosettaMP to predict membrane protein structures. I am currently following the RosettaMP tutorial, which can be found here (https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/membrane-abinitio).

Post Situation: 

Build problem "Never include <bits/libio.h> directly; use <stdio.h> instead."

Category: 
Compilation

Hi everyone,

I am trying to build Pyrosetta from source in Ubuntu 18.04 x64, but  I am having a compilation error, as indicated in the title.

Does anyone have a clue about what could be the issue or has a better idea to compile it?

I am using python 2.7.15, rosetta build 2018.33.60351, ninja 1.8.2, cmake 3.12.1 and gcc 4.8, specified with the global variables: CC=gcc-4.8 and CXX=g++-4.8. The error log is:

Post Situation: 

Problems when working with PTMs - cannot make sugar poses

Category: 
Chemically Modified Residues

Hello everyone,

I have a protein which has a few PTMs in the form of sugars, and I have therefore started experimenting with sugars in PyRosetta. I have found a very nice guide:

https://graylab.jhu.edu/pyrosetta/downloads/documentation/RosettaCarbohydrate_Tutorial-Demo.pdf

which I have used as a starting point together with the documentation e.g.

Post Situation: 

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