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Rosetta Double changing mmCIF chain ID

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: 

Using NCAA

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)

 

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Speeding up FastDesign

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

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.

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

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:

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C-term amidation

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:

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

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.

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Remodel and the depracated EMPTY NC

Category: 
Design

I am using Remodel and I wanted to use a non-canonical amino acid. However, EMPTY NC XXX in the blueprint no longer works as I get an error (below), with a suggestion to use a PackerPalette via a PackerTask or TaskFactory.

I am using Remodel in Pyrosetta 4 2020.49 release (a stable)  for 3.7, but I believe my problem is Rosetta in general one, not a Pyrosetta one. RemodelMover does not accept a task. Furthermore, the pose index numbers change relative to the initial pose so I am not quite sure how such a task would look like.

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