You are here

Home

Design

How to make .frags files

Submitted by krosika1 on Thu, 2021-07-08 18:16
Category: 
Design

Hello! 

I am working through the online pyrosetta tutorial in jupyter notebooks, and they request you use files that are ".frags" files for ab initio structure prediction. Unfurtunately, all of the google drive files that come with the tutorial are no longer accessible (the link goes to a 404 error).

How do you create these .frags files for your POI? I tried using old robetta, but none of the "fragment" files produced have the .frags extension, nor can any of them be downloaded off of the internet. I would appreciate any help/advice!

Post Situation: 
Unsolved
Forums: 
PyRosetta - Scripts

Rosetta Double changing mmCIF chain ID

Submitted by Victor Tobiasson on Thu, 2021-05-13 07:57
Category: 
Design

Hi everyone!

Perhaps a beginner question. I am having problems with Rosetta changing the default chain ID (double letter) when reading and writing as mmcif. Specifically I am relaxing a long list of proteins into cryo-em density using rosetta scripts and and the resulting mmcif files written by rosetta have the "auth_asym_id" truncated from ex. "Ac" -> "c" or "Xm" to "m". Does Rosetta not support double letter chain IDs internally? Is there any solution to this problem?

Best and thank for any help,

Victor

Post Situation: 
Solved
Forums: 
Rosetta 3 - General

Using NCAA

Submitted by ate on Sat, 2021-05-01 02:22
Category: 
Design

I am trying to build peptide sequences containing NCAA to use for FlexPepDocking. After getting params file and rotlib file, when I am using fixbb to do mutation , I encounter with this error “COULD NOT FIND TORSION PARAMS FOR 30 30 6 31”  it shows there is no parameters for C-N-C-CA

I would really appreciate it if someone could let me know how I can build my peptide sequence containing NCAA without ignoring this torsions (i.e., importing 0      1 180.00 for related parameter in mm_torsion_params.txt)

 

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Speeding up FastDesign

Submitted by ebetica0 on Wed, 2021-04-28 13:08
Category: 
Design
<ROSETTASCRIPTS>
  <SCOREFXNS>
    <ScoreFunction name="r15" weights="ref2015.wts"/>
  </SCOREFXNS>
  <RESIDUE_SELECTORS>
    <True name="full_pose"/>
  </RESIDUE_SELECTORS>
  <TASKOPERATIONS>
    <ResfileCommandOperation name="rescmd" command="ALLAA EX 1 EX 2 EX_CUTOFF 1" residue_selector="full_pose"/>
  </TASKOPERATIONS>
  <MOVERS>
    <FastDesign name="design" scorefxn="r15" task_operations="rescmd" repeats="3">
Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Should I be stripping water molecules from my input structure for Rosetta Design?

Submitted by chrisHKL on Wed, 2021-03-24 14:22
Category: 
Design

So I've ran my fixbb rosetta design script and have been happily doing some analysis work, but it just occured to me that I had stripped all the water molecules from my input protein structure and I'm curious whether that biases the rosetta design in a negative way.

What I want to do with my project is to take a fixed-backbone structure of my choosing, optimize the sidechain identities using Rosetta, and then ultimately express it in a cell to see if the optimized sequence folds back into the original backbone conformation.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Can't generate a cst file to use with ddg_monomer application

Submitted by ctqwong on Sat, 2021-03-13 03:53
Category: 
Design

Hi everyone,

I would like to create some double mutations in my protein and thought to get a prediction of the ddG change using Rosetta's ddg_monomer application. I tried running the preminimization using:

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

C-term amidation

Submitted by tttt on Tue, 2021-03-02 07:46
Category: 
Design

Hello,

I have been trying to use the Cterm_amidation patch, but everytime I use it in FastDesign or scoring it turns it back into a regular C terminus.

I've read the posts from other users, but I still can't make it work... What am I doing wrong?

Things I've tried so far:

I added "-include_patches Cterm_amidation" flag, both with the input file having a regular C terminus and with a neutral terminus - in this case I made sure the names of the atoms matched these in the patch:

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Running RosettaScripts, but got an error "src/utility/options/OptionCollection.cc, line 1153, No values of the appropriate type"

Submitted by zhoubin on Sun, 2021-02-28 08:51
Category: 
Design

Hello,

I'm a new user wants to run a RosettaScripts with disulfize mover, but right after I start the scripts, I got the following crash report. Any comments or suggestions on how to solve the issues? Thanks a million.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Pages

Subscribe to RSS - Design