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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: 

Output and Input Tutorial

Category: 
Scoring

 After I had moved to the input_file directory following the Controlling Input and Output in Rosetta,I ran,

$ROSETTA3/bin/score_jd2.default.linuxgccrelease -in:file:s input_files/1qys.pdb

and I got the output,

-bash: /bin/score_jd2.default.linuxgccrelease: No such file or directory. 

What would you recommend doing?

Post Situation: 

Compiling Rosetta using Scons.py

Category: 
Compilation

Hello,

I downloaded Rosetta 3.12 linux + binaries and I noticed the the bin folder contained all 0 kb linuxgccrelease files. I have tried to compile Rosetta using the provided SCons version that was provided with Rosetta 3.12 linux + binaries download. I followed the "Compiling Rosetta" instructions from the user guide and executed the command 

$ python3 ./scons.py -j 4 mode=release bin

Post Situation: 

How to add new Movers to Rosetta

Category: 
Docking

I have a folder with some files to define a mover 'AddEncounterConstraintMover' the Path of the folder is  under 'source/src/devel'. What should I do to make Roseta 'read' the files and apply the mover when its runninng? I have all .hh, .cc, .fwd.hh and Creators files.

Post Situation: 

Antigen-antibody modeling

Category: 
Loop Modeling

I was getting an error while running the snugdock that I solved using the clean_pdb.py command. When I ran flags file using snugdock @flags file, another error came up saying "the antibody doesn't contain start or end of residue of cdr loop H1. Please check pdb is renumbered properly and passed -numbering scheme option matched the PDB.This could also mean missing density in the cdr loop. Loop modeling application can be used to fill missing residues."

Post Situation: 

protein binder interface design error

Category: 
Design

Hi! I ran into a problem when I was repeating the article "Design of protein binding proteins from target structure alone". The protocol I was followed is cao_2021_protocl_guide.txt. The step I was running is 12th: running a pilot job which is a protein interface design. could anyone help solve this problem?

Post Situation: 

Pepspec - sequence sampling

Category: 
Design

Hello,

I am using Pepspec to optimize a 10mers peptide sequence to better binding to a membrane protein. In the design, I kept the first residue constant, while mutating the rest by all 20 amino acids. The flags file is the following:

-in:file:s ppk_complex_0001.pdb

-pepspec::pep_chain B
-pepspec::pep_anchor 1
-pepspec::n_append 9
-pepspec::n_peptides 10000

Post Situation: 

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