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Structure not changing after pose.set_phi

Submitted by publicclass on Thu, 2020-11-05 09:34
Category: 
PyRosetta

Hi, I am trying to implement the Generalized Simulated Annealing routine (Tsalis et al, 1996) and apply it on folding processes.

To do so, I code the mover w.r.t. dihedral angles (each step phi and psi sufer a small, guided perturbation). I am using the pose.set_phi and .set_psi methods to modify pose coordinates. 

The problem:

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PyRosetta - General

WindowsError: [Error 32]

Submitted by jetu20 on Sun, 2020-10-11 21:02
Category: 
Enzyme Design
PyRosetta

I am trying to use IntearctiveRosetta on windows 10 environment and have zero knowledge about coding.....could anyone help me to solve this error......which comes up when I do a position scan using IntearctiveRosetta.....

Traceback (most recent call last):File "scripts\daemon.py", line 2024, in daemonLoopdoPMutScan()File "scripts\daemon.py", line 503, in doPMutScanos.rename("scanprogress", "scanoutput")WindowsError: [Error 32] The process cannot access the file because it is being used by another process

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PyRosetta - General

PyMOL not displaying mover input

Submitted by Butterdream on Thu, 2020-10-01 02:50
Category: 
PyRosetta

Hey there.

I run a Linux subsystem (Linux 4.19.128-microsoft-standard x86_64) on Win10 (Build 19041.508) with wsl2 and Ubuntu 20.04.1 LTS. I successfully installed PyRosetta 4 (python 3.8 release 265).
Python: 3.8.2

On my windows I installed Pymol 2.4.1 198.

If I tell PyMOL to execute the PyMOL-RosettaServer.python3.py script from PyRosetta folder,
-> run \\wsl$\Ubuntu-20.04\home\[User]\PyRosetta4\PyMOL-RosettaServer.python3.py

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PyRosetta - Build/Install

"Server Could Not Be Reached" although I have an Internet connection

Submitted by epi89 on Mon, 2020-09-28 21:32
Category: 
PyRosetta

I am a new user of Interactive Rosetta, I use the software as guided in the tutorial. But when I want to "Thread" my protein, it came up with the message "Server Could Not Be Reached". I have already tried with several different Internet connection, but it still came up with this message. May I know how can I solve this problem? Thank you! 

 

Description of the message: 

The comparative modeling job could not sent to the server! Verify that you have an Internet connection and that the server is running.

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PyRosetta - General

trRosetta modelling with a ligand

Submitted by ShiranBZ on Tue, 2020-08-25 01:44
Category: 
PyRosetta

Hi all,

 

I am trying to modify the trRosetta scripts to run it with a ligand (heme; I added few distance constraints between the protein residues and atoms in the ligand).

I ran molfile2params with the -c flag and have both centroid and full atom params and pdb files of the ligand. I inserted the ligand to the pose and converted it to centroid mode for the initial folding calculations. When I add my ligand constraints prior to the minimization stage, after all the network constraints are read, I get the following error:

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PyRosetta - General

Calling SnugDock from PyRosetta

Submitted by shruthi.murali on Wed, 2020-07-29 15:10
Category: 
Docking
PyRosetta

I am very new to the PyRosetta platform and was hoping to get some guidance on how I can do a SnugDock run from the PyRosetta interface with an antibody pdb and antigen pdb, as I know that the ROSIE queue can be quite long. I've seen the PyRosetta 4.0 documentation for SnugDock but am a little bit overwhelmed as I'm not too well versed in Python. Any level of guidance would be greatly appreciated! 

 

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PyRosetta - General

Segfault when loading scorefxn() and load_from_pdb()

Submitted by mm on Wed, 2020-07-22 03:00
Category: 
Scoring
PyRosetta

Hi,

I am trying to load a structure from PDB and then calculate pairwise residue energies between residues in the structure. For this, I want to first load the scorefxn and then the structure (or viceversa), but whenever I try, either of them gives me a segfault, i.e. if I do scorefxn = get_fa_scorefxn(); pose_from_pdb() the latter crashes and if I do the opposite, get_fa_scorefxn() crashes. 

 

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