You are here

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: 

High Resolution Docking with DockMCMProtocol

Category: 
Docking

Hello, I am working on protein-protein docking with a fairly refined (fastrelaxed) experimental complex.

As such, high resolution docking seems to be the way to go, but I'm a little bit confused with which class to use in pyrosetta.rosetta.protocols.docking :

- Can't get DockingHighRes() to work (RuntimeError: Tried to call pure virtual function "DockingHighRes::apply")

- Pyrosetta Notebooks hint at DockMCMProtocol, but I'm not sure whether this should be used alone, or in conjuction with 

Post Situation: 

Membrane Abinitio modeling error

Category: 
Structure prediction

Hi,

I am modeling a 178 residue membrane protein sequence using the abinitio protocol

To briefly describe what I have done:
1. generate structure fragments using Robetta server
2. generate a span file using OCTOPUS server and the script, octopus2span.pl
3. generate lipophilicity prediction file (.lips4 file) using run_lips.pl

4. generate PDB using membrane_abinitio2.linuxgccrelease

I can run the BRD4.fasta in the tests successfully following above protocols.

Post Situation: 

location of define_interface.py

Category: 
Design

Hello,

I am following the protein design steps presented in the Dr Mieler lab. One of the steps is to generate resfile with  define_interface.py script. I checked my rosetta/tools/protein tools/scripts path, but there is not such a file. Where can I find this script?

Thank you

Post Situation: 

Help with filtering (Rosetta scripts)

Category: 
Design

Hello

I'm running running a pilot ROSETTA script to get the GreedyOptMutation mover with the ddg filter to work. But I get this error message;

ERROR: ERROR: No acceptable mutations found. All possible mutations failed at least one filter!

Any ideas on how to get the filter to allow trajectories with mutations that improve ddG and increases affinity between the 2 proteins contained in the .pdb?

My .xml looks like this:

 

<ROSETTASCRIPTS>

Post Situation: 

Unable to successfully compile using Ubuntu 18.04.5 LTS

Category: 
Compilation

Hello,

I am currently unable to correclty compile Rossetta in a Ubuntu 18.04.5 LTS system.

The version I am currently using is Rosetta 3.12.

Then try to compile using with the following...

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

The following terminal output and error are given:

Post Situation: 

ERROR: Unable to fill in missing atoms.

Category: 
Docking

Could you please help with the following issue (I am using rosetta3.12/rosetta_bin_linux_2020.08.61146_bundle):

core.conformation.Residue: [ ERROR ] Cannot build coordinates for residue TGT at position 111: missing too many atoms. core.conformation.Residue: [ ERROR ] Missing atoms are: C11 N1 C20 C9 C10 C17 N3 N2 C13 C2 N4 C19 S1 C14 C3 C15 C4 C18 C16 C7 C5 C12 C1 C6 C8 H1 H9 H16 H17 H18 H19 H20 H6 H7 H8 H10 H11 H12 H13 H14 H15 H4 H2 H3 H5

Post Situation: 

pepspec anchor dock

Category: 
Compilation

I type the following command :

/Users/andreserobian/rosetta_workshop/rosetta/main/source/build/src/release/macos/10.14/64/x86/clang/10.0/default/pepspec_anchor_dock.default.macosclangrelease @dock.args -corrections::restore_talaris_behavior

 

 And I get this error:

[FILE]: src/apps/public/pepspec/pepspec_anchor_dock.cc
[LINE]: 500
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: no ref pdbs loaded!

Post Situation: 

Extracting PDBs from a Silent file: "Can't find residue type for ARG"

Category: 
Structure prediction

Hello everyone,

I am refining protein structures into Cryo-EM maps, and my output is a silent file. Currently, I am attempting to extract the pdbs from the silent file so that I can analyze and score the structures. The protein has a missing loop, and it is failing on the C-terminus right before the missing loop. Specifically, my error for each structure is "ERROR:  can't find residue type for ARG:CtermTruncation at pos 114 in sequence G". 

Post Situation: 

Pages

Subscribe to RSS - Unsolved