# PyRosetta

## Installation of Rosetta on Mac BigSur

Category:
PyRosetta

Hi,

I have installed pyrosetta and rosetta on my system and when I try to import in my python code it says module not found. I have a BigSur mac computer. Is it because of my system? Can someone help me who has also installed it on bigSur?

Best,

Rashmi

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## restricted fast relax changes whole structure?

Category:
PyRosetta

Hello,

i am trying to do a relax of a certain area of my protein, however, it seems as though the entire backbone moves (and the free energy of the entire system drops dramatically, an other indication the entire thing is beeing relaxed). My code is as follows:

working_pose = pose.clone()
sfxn = create_score_function("ref2015_cart")

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## pyrosetta die slow

Category:
PyRosetta

I'm running a python script with minmover function. After pressing Ctrl + C， the program dies in about 30 seconds. I don't know why it takes so long. Is there a way to kill the job immediately ?

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## Pyrosetta score protein structures with missing atoms in sidechain

Category:
PyRosetta

I have a question regarding Pyrosetta. Currently, I want to use pyrosetta to score some protein structures but with missing atoms in sidechain. So my protein structures contrain full-atoms for backbone but missing one or two atoms per residue on sidechain. I used pose_from_pdb to read my protein structure (pdb). But it seems pysoretta will fill in the missing atoms according to rotamer library. Is there a way to prevent it so I can just score my structures with missing atoms on sidechains?

Thanks a lot for the help,

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## Best way to store a pose by Pyrosetta for Pyrosetta

Category:
PyRosetta

A pose can have a constraint set, a modifiable residue set, an unnoticed pose.pdb_info().obsolete() == True case, virtual residues, energies and a few more. Therefore when saving to disk none of the following truly work as they save coordinates:

pose.dump_pdb('foo.pdb')
pose.dump_scored_pdb('foo.pdb', pyrosetta.get_fa_scorefxn())
pose.dump_cif('foo.cif')
pose.dump_mmtf('foo.mmtf')
pyrosetta.io.poses_to_silent([pose], 'foo.silent')

So I was hoping for an all-in-one

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## How to relax glycans after glycosylating sites on a pose?

Category:
PyRosetta

For reference, I am using the 3.8 Version of PyRosetta.

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## Problem importing residue params file

Category:
PyRosetta

I have been trying to load 'HYP.params' for the hydroxyproline residue. According to previous answers in the forum there are 2 options: add the params file to the residue_types folder and editing the residue_types.txt or loading the params file via command lines in pyrosetta. Neither of these options work for me and raise the following error:

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## Is there a side-program enabling us to see the clashes and interactions between ligand and protein?

Category:
PyRosetta

I'm currently working on a program where i may need to see clashes and interactions between ligand and the protein after PyRosetta-lead conformation. Is there such program?

Thanks!

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