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Structure prediction

RosettaAntibodyDesign: How can I run the protocol without allowing design?

Category: 
Structure prediction
Docking
Design

Hi there,

I am trying to use RosettaAntibodyDesigner without allowing any design elements of the protocol to occur. I understand 100% that this would remove the intended purpose and use cases of RAbD, however, I am trying to piecemeal a side-by-side comparison of a designed mAb (which works reat through this protocol) and a non-designed mAb. 

However, I would like to ensure that both my simulations are executred identially otherwise. (ie., loop flexibility in docking, etc).

Is there any way to runn RAbD while FIXing all the CDRs?

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Modelling temperature dependent RNA structures

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

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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How to fold-and-dock in PyRosetta?

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...)

Post Situation: 

Transmembrane helix fold-and-dock?

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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How to specify constraints during fold-and-dock?

Category: 
Structure prediction
Docking
Constraints
Symmetry

I'm folding a protein which is a trimeric long helix bundle.  I started from the main/demos/public/symmetry_examples/fold-and-dock/ and added my info (sequence, fragments etc).  This basically works but a lot of the resulting folds are globular not long - the helixes fold over on themselves.  I'd like to constrain this to extended conformations only.

I looked at constraints in the Rosetta docs, and tried creating input_files/constraints.cst to give a penalty to any structure which has less than 50-70 A distance between residues 1 and 63:

Post Situation: 

How to run partial_thread in RosettaCM when residure are more than 9999?

Category: 
Structure prediction

One step in RosettaCM is 

partial_thread.default.linuxgccrelease -in:file:fasta JN254802.fasta -in:file:alignment JN254802_5tx1.grishin -in:file:template_pdb 5tx1_clean.pdb

But there are more than 9999 residues in the JN254802.fasta. The output "5tx1_clean.pdb.pdb" writes residue number 10000, 10001, 10002, etc as 1000, because only four positions are allowed for residue numbering (see the example in the end of this post).

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Template/Input length mismatch error during RosettaCM

Category: 
Structure prediction

Hi,

I'm trying to generate homology models for metalloproteins.  I'm working with a test case right now to keep things as simple as possible, and  I'm getting this error which I cannot figure out:

protocols.hybridization.FoldTreeHybridize: [ ERROR ] Template 2 has a residue with PDB number 262 but the input protein only has 261 residues.

Post Situation: 

AbinitioRelax crashed issue

Category: 
Structure prediction

Hello

      I was trying to run AbinitioRelax for structure predictions with attached flags file. The program crashed with the message "Segmentation Fault"

 

##############################################################################################################
#
# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/
# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py
#

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