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Rosetta Remodel - Error in core::conformation::Conformation::residue(): The sequence position requested was 0.

Submitted by daniloboskovic on Fri, 2019-11-08 08:24
Category: 
Design

Dear caretakers/kind strangers,

I ran into an error that i do not understand when trying to do de-novo modelling of a helix linker using REMODEL. When i leave the blueprint file without any new residues it runs fine. But when i add new residues at the end (C Terminal) the program recognizes it is a C terminal extension, but throws this error. 

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Rosetta 3 - Applications

Symmetry mode in Remodel for N-terminal extension

Submitted by yvonne.chan2 on Mon, 2019-11-04 13:41
Category: 
Design
Loop Modeling
Symmetry

Hello, 

I am trying to use Remodel for N-terminal extension of my homotetramer. I am passing in a single subunit (chain A) and symmetry file (4 subunits identified) with my blueprint with the extra residues of interest. I am getting the following error: 

File: src/protocols/loops/loops_main.cc:253
[ ERROR ] UtilityExitException
ERROR: Can't build a fold tree from a loop with an unspecified cut point.

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Rosetta 3 - Applications

Errors in Interface design  

Submitted by Kazu on Thu, 2019-10-31 17:48
Category: 
Design

Hello there, Now I'm trying to optimize the protein sequence at binding interface for increased affinity to its target. A complex structure was previously solved by X-ray crystallography (PDB 3rh8). To make their affinity higher, I would like to design the protein sequence at both sides. Meiler Lab provides a step-by-step tutorial at his website (http://www.meilerlab.org/index.php/rosetta-tutorials). According to his tutorial, I tried, but I found something like error.

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Rosetta 3 - General

running in MPI mode and multiple scores per output PDB file?

Submitted by dantimatter on Wed, 2019-10-30 09:42
Category: 
Design
Scoring

Hi Forum 
I recently did a Rosetta fixbb run with MPI and found that the score file had a lot more lines of output than there were actual PDB files. Specifically, I've got 353 scores in score.sc but only 12 PDB files.  is it possible that the parallel processors are simply overwriting the PDBs?   Is there a flag I should be including to avoid this? 

Thanks!  

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Rosetta 3 - Applications

Alanine Scanning for 1 Protein (no interface)

Submitted by mags33 on Fri, 2019-10-25 10:08
Category: 
Design
Scoring
Enzyme Design

Hi, does anyone know how to do alanine scanning for just one protein?

I looked at different movers for RosettaScripts, like ddgScan, AlaScan, and ddg. Can any of these be used for a single protein with no interface? I want to see which protein residues are good targets for mutation.

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Rosetta 3 - Applications

cryptic error "Got some signal... It is:15" -- an issue with 'fixbb', or something else?

Submitted by dantimatter on Wed, 2019-10-16 14:59
Category: 
Design

Hello Forum

I'm trying to run fixbb on my cluster here, and everything seems to have been going well for a while, but it suddenly stopped and spit out the following in the log file:

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Rosetta 3 - Applications

Segment File Gen - no ouput

Submitted by CATarr on Wed, 2019-10-09 19:05
Category: 
Design

I am in need of some major help. 

I am running the SEWING application because I am copying the secondary structures that fit onto a particular primer, and some key binding residues are located on the loop between two beta strsnds - so I need to generate a new segment file with a few beta strands. 

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Rosetta 3 - Applications

Error with RosettaAntibodyDesign when running antibody_designer.linuxgccrelease

Submitted by bdzhh on Tue, 2019-09-17 17:02
Category: 
Design

Dear friends,

As a new learner of rosetta, I encountered an error "chain_id A represents more than one chain!" after I downloaded the 5ugy.pdb file from RCSB PDB database and renumbered to the AHo Scheme with PyIgClassify Server.

If anyone can help me with this issue? Any help would be appreciated.

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Rosetta 3 - Applications

protein surface design

Submitted by tatsiana.bylund on Sun, 2019-09-15 03:44
Category: 
Design

I'm running FunFolDes on a template and the generated models have very hydrophobic surfaces. They used human-guided design to introduce charged/hydrophilic mutations on the surface. Is there an automatated way to favor charged/hydrophobic mutations on the surface to begin with?

has anyone used https://www.rosettacommons.org/docs/latest/rosetta_basics/scoring/AACompositionEnergy for this purpose?

 

thank you!

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Rosetta 3 - General

Do partner1 and partner2 in mover BackrubDD mean chain1 and chain2 respectively?

Submitted by johnnytam100 on Fri, 2019-08-23 21:10
Category: 
Design

I was doing the design of a protein interface. The starting structure was two chains in contact with each other.

Previously I have tested turning on and off partner1 and partner 2 of BackrubDD, so what I understood from the design behavior was:

partner1="0" -> no flexible design of chain 1 backbone
partner1="1" -> with flexible design of chain 1 backbone
partner2="0" -> no flexible design of chain 2 backbone
partner2="1" -> with flexible design of chain 2 backbone

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Rosetta 3 - Applications

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