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farfar2 failed

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

Post Situation: 

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

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 ??
 

Post Situation: 

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

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!

Post Situation: 

Structure Prediction of protein mutant using relax

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.

Post Situation: 

Problem importing AlphaFold PDB

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...".

 

Post Situation: 

Access to Rosie via GitHub Authentication

Category: 
ROSIE

Dear colleagues.

Would you like to verify my academician e-mail for access to Rosie via GitHub Authentication?

My institution is Taras Shevchenko National University of Kyiv (Kyiv, Ukraine).

Our main academician domain is @knu.ua.  Our additional (old) domain is @univ.kiev.ua.

Sincerely

Alex Nyporko

Post Situation: 

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