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Access to GitHub Denied

Submitted by Lucia_G on Wed, 2023-01-25 07:13
Category: 
ROSIE

Hi,

I am contacting you as I cannot login in GitHub portal with my ROSIE account credentials to perform docking analysis. 

My credentials are:

Lucia93

University of Warwick

I also created an account on Rosetta Commons website, but neither those ones are accepted for the login.

Can someone help me with this please?

Best wishes,

Lucia

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Unsolved
Forums: 
ROSIE - General

farfar2 failed

Submitted by Kamonwan on Mon, 2023-01-23 18:41
Category: 
Structure prediction

Hello

I am trying to model a modified 3D RNA structure using farfar2. 

Job 「№108206」has failed with the message: No output silent files were produced in the FARFAR2 step; please double-check your inputs!

I have checked the input sequence and dot bracket files (PDB file exceeds the maximum allowed size for upload). I don't know, how to solve it. Attaching the input flies. Could someone please help me sort the error.

Thank you

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Unsolved
Forums: 
ROSIE - General

Grafting using antibody.mpi.linuxgccrelease and specifying custom template which doesnt have pdb id.

Submitted by SubhaK on Wed, 2023-01-18 23:33
Category: 
Structure prediction

Hello all,
Using this command to graft from a specific template
antibody.mpi.linuxgccrelease -antibody:blastp /home/rosetta/ncbi-blast-2.13.0+/bin/blastp -fasta antibody.fasta -antibody:h1_template  pdb_id

Can we use the same approach for grafting where we dont have a pdb id to specify template and use a specific structure instead ??
 

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Forums: 
Rosetta 3 - Applications

snugdock(sequence position requested was greater than the number of residues in the pose)

Submitted by lei on Thu, 2023-01-12 01:40
Category: 
Docking

Dear users, 

When I did snugdock, my native input structure and snug input structure share the same number of residues and residue indexes, but the error still shows up "sequence position requested was greater than the number of residues in the pose".
I attach both files and appreciate any suggestion. Thanks!

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Forums: 
Rosetta 3 - Applications

Structure Prediction of protein mutant using relax

Submitted by Delfosse57 on Tue, 2023-01-10 13:26
Category: 
Structure prediction

Hello,

I am attempting to predict the structure of a metalloenzyme after 5 mutations using the relax function. My current protocol consists of adding the following:

- Adding a mutation to the protein in pymol

- Relaxing the protein and picking the lowest energy structure

- Adding another mutation to the lowest energy structure and repeating until all mutations have been added.

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Forums: 
Rosetta 3 - General

Problem importing AlphaFold PDB

Submitted by Rick Neubig on Mon, 2023-01-09 09:48
Category: 
PyRosetta

I have tried to import a PDB that came from an AlphaFold Docking run. I have repaired it using the PRAS server to add the OXT lines (file attached) but it still won't import. Here is the script for import followed by the first lines of the results with the error messge "discarding 4 atoms at position 1 in...".

 

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Forums: 
PyRosetta - General

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