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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")

Post Situation: 

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

Post Situation: 

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. 

Post Situation: 

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