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"corrupted" small molecules. aromatic rings get distortet during relax

Category: 
PyRosetta

Hello, i am trying to relax an enzyme with a co-factor (nadp) but whenever I do, the resulting structure looks wrong.

I use the NADP structure from pubchem as a starting point, then molfile2params structure  and copy paste the returned LG_0001.pdb to my protein. 

i then run the following code:

Post Situation: 

CONECT information for PDB files by raw sequence

Category: 
PyRosetta

Hello,

I create a pose from sequence and dump it as PDB:

pep_pose = pyrosetta.pose_from_sequence(sequence, res_type='fa_standard', auto_termini=True)
# pep_pose = pyrosetta.Pose()
# pyrosetta.rosetta.core.pose.make_pose_from_sequence(pep_pose, sequence, 'fa_standard', auto_termini=True)
pep_pose.dump_pdb(pdb_file_path)

As I understood, 'pose_from_sequence' creates a peptide structure by sequence, but what I found was that the PDB file misses the whole CONECT information.

Post Situation: 

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: 

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