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Challenge with applying AntibodyCDRGrafter method and MinMover method

Submitted by kylevaccaro on Sat, 2023-02-18 21:41
Category: 
PyRosetta

I've been trying to trial designing antibody CDRs. Thus far I haven't had much luck applying standard methods. I've converted my antibody to AHO scheme with PyIgClassify and applied the cleanATOM method, however, I am still running into the following error prompt. Any recommendations on how to resolve this, would be great.

I've applied the AntibodyInfo method and am able to print the antibody with the sequences of each CDR, so I don't think the first portion about start and end not being contained is correct.

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PyRosetta - General

How to use pyrosetta to generate decoys of RNA with different RMSDs (e.g. 1Å, 5Å, 10Å).

Submitted by Alice123 on Fri, 2023-02-17 18:24
Category: 
PyRosetta

Hi

I am a beginner in pyroseta and now need to use pyrosetta to generate decoys of RNA with different RMSDs (e.g. 1Å, 5Å, 10Å), I checked the manual but it is still not clear, can you give me some guidance, thank you!

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PyRosetta - Applications

ligand_docking

Submitted by yang on Thu, 2023-02-16 04:37
Category: 
Docking

Hi , I'm beginner to Rosetta . In ligand_docking , it is said "chain_id F does not exist" . There are two ligands and one receport to dock ,   I can not define chain F or chain X (in my dock.xml).  I can not undersstand  some answers about this question. I wish receive the answer.

 

the process in ligand_docking:

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Rosetta 3 - Applications

Rosetta remodelling - how to change the added residue type instead of just VAL

Submitted by xuezhi on Wed, 2023-02-15 14:00
Category: 
Design

Dear sir,

I am new to Rosetta. I followed the rosetta protocol to pad a few residues to N, C terminals of my protein. I follow the remodel.static.linuxgccrelease instructions. Created pad.bd as below. Then I run "rosetta_bin_linux_2021.16.61629_bundle/main/source/bin/remodel.static.linuxgccrelease -in:file:s 1mhp_H_0001.pdb -remodel:blueprint 1mhp_padpadded   -remodel:dr_cycles 1 -num_trajectory 1 -save_top 1" . but it only added Val reisidues. I want to added non-specified residues but not all into VAL. how to fix this? Kind regards.

 

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Rosetta 3 - General

How to set jump between ligands

Submitted by Zehui Zhou on Wed, 2023-02-15 04:48
Category: 
Compilation

Previously, I want to add spin to the "Initial Perturbation" on protein-protein docking (https://www.rosettacommons.org/node/11700), and I with the second partner spin around the axes of the center of the two ligands. I think using AtomTree can set a jump between the two ligands, so I introduced the SpinMover to control the rotating axis. Can the jump be set between two ligands? Because I got an error when running with modified FoldTree:

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Rosetta 3 - General

Truncating a protein using rosetta

Submitted by Wexter300 on Mon, 2023-02-13 12:05
Category: 
Design

I am a beginner to rosetta, and I was wondering if there is a way to truncate/ get rid of a specific part of a sequence and create a stable protein? I have the PDB of the protein and the specific parts of the sequence I need to truncate. It is to get rid of loops at the terminus. Do I just input a sequence to rosetta with the unwanted parts deleted and have it model the protein ?

Sequence : 

G-SPELREKHRALAEQVYATGQEMLELREKHRALAEQVYATGQEMLKN-TSN

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Rosetta 3 - General

Segmentation fault with nstruct > 1

Submitted by Brian Wiley on Sun, 2023-02-12 20:46
Category: 
Loop Modeling

I am running loop model with the remodel protocol (remodel.static.linuxgccrelease).  It succesfully can model despite ligands in the file using -ignore_unrecognized_res when a single structure is required with -nstruct 1 however as soo as I try to increase it to -nstruct 2 I get a segmentation fault.  Anyone experience this before?

 

 

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Rosetta 3 - General

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