I tried to run the below script in Python to automate some stuff:
Hi,
I am trying to access the cm_scripts that are used in this (http://www.pnas.org/content/109/25/9875) study. Could you please let me know where I can find these scripts?
Thank you very much.
I had a bunch of assembled fragments and I ran the below protocol on them for the fragment assignment and the genration of a consesus trajectory.
#!/bin/sh
$ROSETTA3/source/bin/denovo_density.linuxgccrelease\
-mode consensus \
-in::file::silent round1/assembled.*silent \
-consensus_frac 1.0 -energy_cut 0.05 \
-mute core
# use the old model as a starting point
cp S_0001.pdb round1_model.pdb
Hi,
I am trying to do a de novo protein folding from a protein sequence with repeating Gly and Arg only.
So the sequence looks like GRGRGRGRGR..... I put the sequence onto Robetta Fragment Server and it gave me this error message:
=======================================================================================
I'm new to Rosetta, and trying to figure out how to calculate the ddG of the interaction between Chain A and Chain B (which homodimerize) for all possible substitutions at each residue compared to wild-type (where Chain A and B will always carry the same mutation). Are there any existing packages that will handle this, or what script would you recommend for my situation?
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:
Hi All
is there any way that I can perform the structure prediction using rosetta locally the way we can do on robetta server? I was going though the protocol for comparative modeling but its quite involved. I am looking for something that provide me robetta server kind of automation.
Thank you
Dhiraj
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~
I've done a structure refinement of a protein by Rosetta3.8.
However, I'm not sure that what I've done is correct or not.
The protocol that I followed are list below:
First, I put my protein sequence(.fasta file), torsion angle(predicted by talos+), RDC value(experimental data) into the website( http://robetta.bakerlab.org/fragmentsubmit.jsp) to do fragment generation.
Hi Rosetta Community,
With comparative modeling application I created a silent file output using following flags
-out:file:silent threaded_model.out
-out:file:silent_struct_type binary
Later, when I used the generated silent file as an input for other applications like "cluster" or "score", it crashed with an error.
ERROR: Assertion `is_int( tag )` failed.
ERROR:: Exit from: src/core/io/silent/RNA_SilentStruct.cc line: 292
Is there any easy fix for that?
