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Structure prediction

Grafting using antibody.mpi.linuxgccrelease , the modelled structure does not have constant region of the antibody.

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
The modelled structure does not have constant portion of the antibody.

Post Situation: 

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

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Error when attempting to relax pdb, "flag_input_relax" not found

Category: 
Structure prediction

I am following the rosetta tutorials and run into an error when attempting to relax a pdb for refinement. The "flag_input_relax" file cannot be opened by rosetta, even though I've granted myself full permissions and even changed it into an executable via chmod 755. I made a copy of the file and it could not open the copy either. Below is the command that gives me the error:

 

rosetta/main/source/bin/relax.default.macosclangrelease -in:file:s ~/rosetta/main/demos/tutorials/input_and_output/input_files/from_rcsb/1qys.pdb flag_input_relax

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: 

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: 

Is there a limitation of RNA length using farfar2?

Category: 
Structure prediction

Hi, I recently used farfar2 to predict some RNA structures, but it seems that the longest RNA sequence that would succeed is beneath around 500-600 nt. When I submit sequences with 1800, 2000 or 7500 nt, they failed with returning "No output silent files were produced in the FARFAR2 step; please double-check your inputs!", and I couldn't figure out why. So I wonder is there a limitation of RNA length or size when using farfar2 to predict structures(which I've searched and not found yet), or I just made other mistakes somewhere else. Thanks a lot!

Post Situation: 

undefined symbol: ZN9CifString12UnknownValueE error meaning?

Category: 
Structure prediction

Hello,

I am trying to run mp_domain_assembly protocol via the cluster and getting this error:

/truba/home/aniyaz/softs/rosetta/main/source/bin/mp_domain_assembly.mpi.linuxgccrelease: symbol lookup error: /truba/home/aniyaz/softs/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/mpi/libcore.2.so: undefined symbol: _ZN9CifString12UnknownValueE

After several same rows it ended up with the Exit code: 127

Post Situation: 

Unexpected length of light chain FR1

Category: 
Structure prediction

Hello Rosetta forum,

I recently started using rosetta for building antibody structures and running "antibody.linuxgccrelease -fasta L2251x0566aa.fasta | tee grafting.log" command on my sequences. Seems like the default setting doesn't prefer light-FR1 length >22 ? Any help would be appreciated.

File: src/protocols/antibody/grafting/chothia_numberer.cc:149
ERROR: Unxpected length of light-fr1 [length=23], length expected to be: [19, 20, 21, 22]!

Post Situation: 

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