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Distorted metal coordination geometry after relaxation (SetupMetalMover was used, fold tree and constraints were set manually)

Category: 
Design
Scoring
Constraints
PyRosetta

 

Hello,

I am trying to relax Zn containing peptides like zinc fingers, but always got distorted geometries of the coordination site and much higher scores after the relax. Still, the rest of the peptide looks nice.

Post Situation: 

Problem Installing PyRosetta/InteractiveROSETTA

Category: 
PyRosetta

I am attempting to install PyRosetta/InteractiveROSETTA on my 64bin Debian Stretch Linux platform and have encountered some problems.

Although the installation of InteractiveRoasetta encountered some problems:
 

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All self-test.py tests fail after installation

Category: 
PyRosetta

Hello Rosetta community

I am trying to install Pyrosetta3.7 in Linux-windows. The installation appears to go without a hitch. But then when I run the self-test.py script, all tests fail. Error messages look like the one below

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trans-ACPC

Category: 
PyRosetta

Hello!

I've been trying to create a pose with trans-ACPC, but when I use the X[TAC] in the sequence, it doesn't seem to know what residue it is. I know there's a params file for it... I tried loading a pdb structure with ACPC in it as my pose to see what'd happen and it says that:

"ERROR: Error in core::scoring::methods::RamaPreProEnergy::residue_pair_energy(): The RamaPrePro term is incompatible with cyclic dipeptides (as is most of the rest of Rosetta)."

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Rosetta get_fa_scorefxn()

Category: 
PyRosetta

I am using PyRosetta to minimize several complexes and obtain the rosetta calculated energy values. In order to obtain all the rosetta scoring terms, I am using the get_fa_scorefxn function. Whereas I want to retain all the scoring terms, the only option that seems available to see all of them is with the following lines:

scorefxn = get_fa_scorefxn()

pose = pose_from_pdb(<minimized_complex_pdb>)

scorefxn.show(pose)

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how to download "GUIs/pyrosetta_toolkit/documentation" ?

Category: 
PyRosetta

Hello,

      I need GUIs/pyrosetta_toolkit/ documentation from http://www.pyrosetta.org/documentation#TOC-1.-The-PyRosetta-Toolkit. However the linkage to this documentation is forbidden now. Can someone do me a favour to provide this documentation by email ? My email address is liuhui@qibebt.ac.cn

      Thank you very much!

best wishes

Hui Liu

Post Situation: 

ipython can't find PyRosetta files

Category: 
PyRosetta

I'm trying to get interactive rosetta to work on a linux virtual machine. I have zero experience coding so I've been struggling royally. I first tried Ubuntu 18.04, but after having some difficulty I decided to switch to as close of a setup as what is in the interactive rosetta install video as I could. I tried Ubuntu 12.04 64 bit with python 2.7.3 and PyRosetta 3 release 104. When I try to import rosetta into ipython this appears:

Post Situation: 

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