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Structure prediction

Use membrane or non-membrane weights in RosettaCM for a hexon in virus capsid?

Category: 
Structure prediction

I am using RosettaCM to build a hexon in the virus capsid. The tutorial provides membrane and non-membrane weights in the "Hybridize" step. Should I use the membrane or the non-membrane weights? Are the membrane weights applicable for any membranes?

https://www.rosettacommons.org/demos/latest/tutorials/rosetta_cm/rosetta_cm_tutorial

Here is to show the stage1 weights for membrane and non-membrane

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Rosetta remodel - including an RNA ligand

Category: 
Structure prediction

I have been trying to include an RNA as a ligand for some time now, and every attempt is a failiure. Can someone explain me how to put a whole ribonucleoprotein, RNA as ligand, into remodel? When i get a relaxed structure my interaction sites are messed up. So far i have been using constraints but i really need that RNA in there as a ligand for further research.

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What means "[ ERROR ] TIME_STAMP: AbrelaxMover: finished ...NO_BATCH S_0001."

Category: 
Structure prediction

Dear fellows,

When I generate broker.out-file with a help of minirosetta-application, I get such error:

"[ ERROR ] TIME_STAMP: AbrelaxMover: finished ...NO_BATCH S_0001"

although that script runs smoothly and generates a necessary file.

Could someone explain me, what means this error, please?

I will be sincerely grateful for your response and I am looking forward to it.

Best regards,

Corvin.

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use_truncated_termini not working in combination with params files

Category: 
Structure prediction

When using FastRelax with the keyword -use_truncated_termini true as expected no OXT are added if not present in the input file. However, when I run the same protocol with additional params files (-extra_res_fa), OXT are added to all chains and the -use_truncated_termini seems to be ignored. Does anyone know/suspect a reason for this and might know a workaround?

Thanks,

Georg

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Relaxation vs minimisation

Category: 
Structure prediction
Scoring
PyRosetta

Hi all,

I am very new to the computational structural biology community and I have tried to model a structure by using a software which runs MODELLER on the background. However, my result shows a number of steric clashes and a very high fa_rep when I calculate it with PyRosetta. I am therefore trying to improve the structure before moving on with the rest of my analysis. 

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Comparative Modeling Templates for Protein with Multiple Domains

Category: 
Structure prediction

I want to build the structure of a protein that consists of multiple chains. One of my templates is homologous to the entire protein, but the other templates are only homologous to portions of the protein. I found an early post that suggests manually merging different structures into a sequence that's homologous to the entire protein. Since this answer was posted in 2012, I wonder if is there any new approach to deal with structures that are homologous to different parts of the target?

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Are 100 structures the maximum generated when using homology_with_end_extension (broker protocol)?

Category: 
Structure prediction

Hi!

I have one protein that I would like to model ab initio the final 29 residues (1 - 160 is fixed/I have the x-ray crystallography model,  161 - 189 is the region to be modeled).

I am using the following parameters:

- protein.tpb

CLAIMER RigidChunkClaimer

REGION_FILE protein.region

PDB_FILE protein.pdb

END_CLAIMER

- protein.region

RIGID 1 160 0 0 0

- the command I ran :

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FARFAR2 error

Category: 
Structure prediction
Nucleic Acids
ROSIE

Hi ROSIE and FARFAR2 team,

       I used FARFAR2 to test the 3D structure prediction of several RNAs two weeks ago with native PDB uploaded. But all the jobs were finally dead with the error message "2-rescore_to_native_or_lowest". Could you tell me why this happened? You can find the sequence, 2D structure, and native PDB in the attachment.

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