You are here

Home

Structure prediction

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.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Is there a limitation of RNA length using farfar2?

Submitted by lwb on Wed, 2023-01-04 19:09
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: 
Unsolved
Forums: 
ROSIE - General

undefined symbol: ZN9CifString12UnknownValueE error meaning?

Submitted by aniyaz on Wed, 2023-01-04 08:37
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: 
Solved
Forums: 
Rosetta 3 - General

Unexpected length of light chain FR1

Submitted by mgupta on Fri, 2022-12-09 01:03
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: 
Unsolved
Forums: 
Rosetta 3 - General

Predicting structure of protein after a few mutations

Submitted by Delfosse57 on Thu, 2022-12-01 20:40
Category: 
Structure prediction

Hi all,

I am attempting to predict the structure of a protein after mutating a couple residues (4-5). I have the wildtype structure so I have been adding the mutations one-by-one in pymol, with each single mutation relaxed with the relax function. Is this the best way to use Rosetta to predict such structures? Also, are there any modifications to the relax function that would increase the accuracy for structure prediction?
 

Thank you!

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

On iterations in ddg_monomer

Submitted by Proteinmechanic on Fri, 2022-09-30 21:23
Category: 
Structure prediction

Dear community, 

I am just beginning to explore Rosetta with some mutational analysis. 

Currently exploring ddg_monomer. 

From what I have read so far, ddg_monomer doesn't have parallel support. 

Could I please know if setting 

-ddg::iterations 1

and then repeating the above 49 other times, to make a total of 50 predictions and then choosing the top three stated in the manual would produce similar results as setting 

-ddg::iterations 50

and running only once. 

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Error Fasta file

Submitted by gabrielab on Mon, 2022-08-15 00:41
Category: 
Structure prediction

Hello,

I am trying to predict antibody structure but I keep getting an error message when choosing the fasta file containing the heavy and light chain. I am using the ">heavy" and ">light" marker in the fasta file but it doesn't seem to recognise the sequences. I am not sure what I am doing wrong. I am attaching an image of the error message for reference. 

Thanks for your help!

Post Situation: 
Unsolved
Forums: 
ROSIE - General

ERROR: Your compiler does not have full support for C++11 regex, and therefore can't support RegEx_based_CDR_Detector/antibody g

Submitted by yliang20 on Mon, 2022-08-08 16:59
Category: 
Structure prediction

Hi there,

I tried to do antibody modeling, however, there is complie issue shown as the following:

$ROSETTA/bin/antibody.linuxgccrelease -fasta 27666.fasta | tee grafting.log

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Pages

Subscribe to RSS - Structure prediction