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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

Comparing a prediction to the native structure and calculate RMSD for RNA

Submitted by danwolf_33 on Thu, 2023-02-09 09:32
Category: 
Nucleic Acids

Hi all,

I am new to Rosetta and FARFAR2. I have attempted modelling the structure of PDB:1KXK using the following command line:

rna_denovo -sequence gucuaccuaucgggcuaaggagccguaugcgaugaaagucgcacguacgguucuaugcccgggggaaaac -cycles 20000 -nstruct 3 -bps_moves false -minimize_rna true -secstruct ".....(((.((((((...(((((((((((((((....))))))..)))))))))..)))))))))....."

Now I want to compare the obtained structure to the original PDB and to calculate the RMSD. I ran the following:

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Rosetta 3 - Applications

Applying RMSD constraints using pyrosetta or Rosettascripts

Submitted by chenna on Thu, 2023-02-09 05:37
Category: 
Constraints

Hello all,

I'm interested in applying RMSD constraints to a pose using pyrosetta.

I currenly have a native pose which is deformed manually, such the the backbone RMSD with respect to the native is 1 Angstroms. 

pose.residue(r).set_xyz(a, py.rosetta.numeric.xyzVector_double_t(new_coords[0], new_coords[1], new_coords[2]))

However, when I relax (cartesian), I notice the structure relaxing back to the native, ie the RMSD decreases to ~0 Angstroms.

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PyRosetta - General

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