Unsolved

I created a fragment file of my structure using Robetta, the link to the results is right here http://robetta.bakerlab.org/fragmentqueue.jsp?id=51178. I'm using the

fragment file to do density guided structure prediction as described in the paper "De novo protein structure determination from near-atomic resolution cryo-EM maps". 

I'm trying to run the code below:

So I'm trying to load this ligand_protein complex PDB into PyRosetta by temporarily creating a ResidueTypeSet

from pyrosetta import *

init()

params_path = Vector1(['cefotaxime.params', 'cefotaxime.params'])

nonstandard_residue_type = generate_nonstandard_residue_set(params_path)

I got this error message:

generate_nonstandard_residue_set() takes exactly 2 arguments (1given)

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.

Hi all. 

I want to predict the effect of a point mutation in a protein stability. I have the .pdb crystal structure of the wild type.

After a literature search, I think this paper presents the most comprehensive study of different methods for this analysis DOI:10.1002/prot.22921. So I want to do the prediction using their protocol 16. I also found python code for this protocol here: https://github.com/Kortemme-Lab/ddg/tree/master/protocols/ddg_monomer_16.