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PyRosetta

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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ValueError: can only read V2000 format files

Category: 
PyRosetta

I'm providing the molfile_to_params.py with the enzyme-ligand complex of my molecule but unfortunetly it gives the "ValueError: can only read V2000 format files" error. Previously i gave it the individual ligand file and it processed with no problems. But when i try to process this file it doesn't seem to work. I suspect the problem is about the chemical table file formats and something in my code is from V3000 but i'm a begginer so i don't know what.

I will attach the text files of both the ligand .mol file and the complex .mol file. 

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How do I insert or delete residues into specific locations?

Category: 
PyRosetta

I want to insert/delete residues in sequences. My goal is to take mutant sequences, have them become similar sequences of the WT and focus on each mutation. Is that possible?

 

Example: ABABA, and I want to insert "C" into the third position so it would look like this ---> ABCABA

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Mutate residue with NCAA

Category: 
PyRosetta

Hello,

I am trying to mutate a pose with beta-amino acid residues. From what I've tried and read, it's impossible with both mutate_residue and MutateResidue mover, because they only take one letter representations of the residues. My hope is that I can figure out how to do it through packing. I'm not sure how to make it work properly.

This was just my test code to see what would work:


pose = pose_from_sequence('A'*20)
test_pose = Pose()
test_pose.assign(pose)

mutant_position = 3

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Structure not changing after pose.set_phi

Category: 
PyRosetta

Hi, I am trying to implement the Generalized Simulated Annealing routine (Tsalis et al, 1996) and apply it on folding processes.

To do so, I code the mover w.r.t. dihedral angles (each step phi and psi sufer a small, guided perturbation). I am using the pose.set_phi and .set_psi methods to modify pose coordinates. 

The problem:

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WindowsError: [Error 32]

Category: 
Enzyme Design
PyRosetta

I am trying to use IntearctiveRosetta on windows 10 environment and have zero knowledge about coding.....could anyone help me to solve this error......which comes up when I do a position scan using IntearctiveRosetta.....

Traceback (most recent call last):File "scripts\daemon.py", line 2024, in daemonLoopdoPMutScan()File "scripts\daemon.py", line 503, in doPMutScanos.rename("scanprogress", "scanoutput")WindowsError: [Error 32] The process cannot access the file because it is being used by another process

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PyMOL not displaying mover input

Category: 
PyRosetta

Hey there.

I run a Linux subsystem (Linux 4.19.128-microsoft-standard x86_64) on Win10 (Build 19041.508) with wsl2 and Ubuntu 20.04.1 LTS. I successfully installed PyRosetta 4 (python 3.8 release 265).
Python: 3.8.2

On my windows I installed Pymol 2.4.1 198.

If I tell PyMOL to execute the PyMOL-RosettaServer.python3.py script from PyRosetta folder,
-> run \\wsl$\Ubuntu-20.04\home\[User]\PyRosetta4\PyMOL-RosettaServer.python3.py

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