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CONECT information for PDB files by raw sequence

Submitted by Fata on Wed, 2022-06-22 01:47
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.

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PyRosetta - Scripts

Is this the intended behaviour?

Submitted by Ken on Thu, 2022-05-05 14:59
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

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PyRosetta - General

PyRosetta - PyMOL_Mover problem

Submitted by Stephen P. Molnar on Fri, 2022-03-11 06:50
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)

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Rosetta 3 - Build/Install

CONDA_OVERRIDE_GLIBC=2.27

Submitted by matteoferla on Thu, 2022-03-10 09:59
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:

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PyRosetta - Build/Install

Atom mapping in RMSD functions

Submitted by gkell on Tue, 2022-02-15 15:48
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.

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PyRosetta - General

Questions of Cartesian_ddG calculation in PyRosetta

Submitted by CKS2001 on Fri, 2022-01-07 01:36
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.

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PyRosetta - General

Installation of Rosetta on Mac BigSur

Submitted by rashmijain on Tue, 2021-10-12 15:06
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

 

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Rosetta 3 - Build/Install

restricted fast relax changes whole structure?

Submitted by patcD on Wed, 2021-08-25 02:05
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")

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PyRosetta - General

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