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Is this the intended behaviour?

Category: 
PyRosetta

Hi all,

I am a new PyRosetta user and am running into something weird.  I am playing with some tutorial examples to get my feet wet and here is a very simple question.  When I do the following,

p = pose_from_sequence("Q"*5) 

p.dump_pdb("test.pdb")

I get the the side chain carbonyl oxygen bonded to the backbone (see attached pdb).  Is this the intended behaviour?

Best,

Ken

Post Situation: 

PyRosetta - PyMOL_Mover problem

Category: 
PyRosetta

I have Debian BUllseye installed on my Linux platform

I have installed pyrosetta 2022.09+release.433f0fc py39_0 and pymol-open-source 2.5.0  py39h20a8f2e_4 in a conda environment (Python-3.9.10).

I ma following the PyRosetta - PyMOL_Mover Tutorial and am having a strange problem.

Whew I paste 'cd /home/comp/Miniconda3/envs/PyRosetta/lib/python3.9/site-packages/pyrosetta' followed by 'run PyMOLPyRosettaServer.py' separately I get PyMOL <---> PyRosetta link started! (belwo)

Post Situation: 

CONDA_OVERRIDE_GLIBC=2.27

Category: 
PyRosetta

Not a question, but a note of an issue to save anyone getting lost by it

I had a spot of bother installing PyRosetta on a cluster running Ubuntu as PyRosetta was giving:

lib64/libc.so.6: version `GLIBC_2.27' not found

(Dejavu of pytorch, anyone?)
To fix it the system environment CONDA_OVERRIDE_GLIBC=2.27 does the trick:

Post Situation: 

Atom mapping in RMSD functions

Category: 
PyRosetta

I'm trying to calculate the common heavy atom RMSD between a polypeptide fragment and a variant, but in reading through the various RMSD functions in pyrosetta.rosetta.core.scoring it isn't clear why all_atom RMSD functions don't fail when given two poses which differ by amino acid identity - can anybody explain what's going on under the hood here or direct me to some documentation that details it? Also, do/how can any of the protein RMSD functions specify heavy atoms only as a predicate?

Thanks, I'd appreciate any assistance.

Post Situation: 

Questions of Cartesian_ddG calculation in PyRosetta

Category: 
PyRosetta

Dear All,

I am new to PyRosetta and I am trying to calculate the ddG after point-mutation. The calculation logic is like the following:

1) clean the pdb file and use cartesian relax to minimize its energy

2) perform the point mutation with mutate_residue() function

3) calculate the score before and after the mutation to gain the ddG

However, the ddG data I got was always positive values and have large differences from the benchmark.

Post Situation: 

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?

Thank you in advance!

Best,

Rashmi

 

Post Situation: 

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: 

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