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protein relax

Submitted by Alison_Yajie on Tue, 2020-05-19 08:29
Category: 
Enzyme Design

I am trying to relax my protein with ligands FMN before do further design. I used movemap to exclude the rotamer on FMN. my flag and movemap file looks like below. I also attached my protein_FMN pdb. It takes an extremely long time and it seems like stuck somewhere (I attached the screen shot). Is it normal and anybody knows why? Thanks

flag file:

-in:file:s ./input/3TX9.A_FMN_Crystal.pdb

-in:file:movemap movemapfile

# Harmonic runs

-relax:constrain_relax_to_start_coords

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Rosetta 3 - Applications

Modelling temperature dependent RNA structures

Submitted by tuleshwori on Tue, 2020-05-19 01:16
Category: 
Structure prediction
Nucleic Acids

Hi to all,

I am really new to rosetta. I am using rna_denovo to generate 3D structures of RNA. I believe the default tempertaure used for modelling is 300K. I want to know if we can set our own temperature  for modelling RNA ? I did saw the option of temperature in the -help, written as 2 in the settings option, but I am not sure how to use it. Can we just define the temperature that we want, after writing this option? I am not sure how to go about this.

Please let me know the best way to go about this. And many thanks.

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Rosetta 3 - Applications

RosettaAntibodyDesign] How can I use run_relax and run_snugdock as part of my command and workflow?

Submitted by brspurri on Thu, 2020-05-14 11:15
Category: 
Structure prediction
Docking

I am trying to run a basic antibody/antigen design/dock simulaton using RosettaAntibodyDesign (from Rosetta 3.12)

I am using the command: 

antibody_designer.macosclangrelease \
  -database /path/to/database/ \
  -do_dock \
  -use_epitope_constraints \
  -nstruct 5 -in:file:s complex_renumbered.pdb \
  -seq_design_cdrs H1 H2 H3 \
  -primary_cdrs H3 \
  -mintype relax \
  -run_snugdock \
  -run_relax \
  -out:path:all ./output

 

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Rosetta 3 - Applications

Output "per-residue" energy score to database

Submitted by pedro.guillem on Thu, 2020-05-14 04:22
Category: 
Scoring

Hello all.

I noticed that when I output a relax cycle to a PDB, the residue scores are in the bottom of the PDB.

When I output the results to a database (MySQL), the table structure_scores holds the energy scores of the whole PDB, but I can't find the per-residue values anywhere.

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Rosetta 3 - General

How to fold-and-dock in PyRosetta?

Submitted by sarah_b on Thu, 2020-05-14 02:37
Category: 
Structure prediction
Docking
Symmetry
PyRosetta

I'd like to do something similar to regular Rosetta fold-and-dock but in PyRosetta.  I've looked at D060_Folding.py and D100_Docking.py examples and while I (mostly) understand what each is doing, I have no idea how to combine them.

How to get a foldtree with symmetry? (in my case it's just simple C3) 

How to combine folding and docking?  Just alternate calls to folding.apply(test_pose) and dock_prot.apply(test_pose)?  (It can't be that simple...)

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PyRosetta - General

Multistate design issues with -run:msd_job_dist option and MSDMover

Submitted by elaine.thai on Wed, 2020-05-13 18:07
Category: 
Design

Hi there,

I'm trying to perform multistate design using Rosetta 3.11 to improve antibody binding to five slightly different epitopes. I've been following the tutorial provided by the Meiler Lab and I've been able to successfully prepare my input files, but I'm having issues running the design.

First, when I tried to run the design using the attached .options and .xml files, but I got the following error:

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Rosetta 3 - Applications

Transmembrane helix fold-and-dock?

Submitted by sarah_b on Tue, 2020-05-12 02:09
Category: 
Structure prediction
Docking
Symmetry
Membrane

I'd like to fold-and-dock a trimeric transmembrane domain.  I mostly have the "Fold And Dock" working following the example in demos/public/symmetry_examples/fold-and-dock/.  However this is treating the transmembrane helixes as though they are in solvent (so for example any hydrophilic groups always rotate outwards).  I'd like to do something which is a combination of "Membrane Abinitio" and "Fold and Dock".  Is this possible, and how do I do it?

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Rosetta 3 - Applications

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