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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,

Post Situation: 

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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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:

Post Situation: 

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!

Post Situation: 

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

Post Situation: 

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

Post Situation: 

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