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Mutations are ignored (fixbb) when using -auto_setup_metals option

Category: 
Design

When using fixbb.static.linuxgccrelease (2018 or 2019 release) with the -auto_setup_metals option set, see cmd line below, all mutations to a residue with a link to a metal ion, are ignored in the model generated (PDB file).

Run process: /usr/local/rosetta/main/source/bin/fixbb.static.linuxgccrelease -s ../src_updated_0001.pdb -extra_res_fa ../sub.params -resfile resfile-S100.txt -nstruct 1 -ex1 -ex2 -database /usr/local/rosetta/main/database -jran 1001 -constrain_relax_to_start_coords -use_input_sc -minimize_sidechains -overwrite -auto_setup_metals

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Rosie vip function fails on multiple tries

Category: 
Design

Hi:

 

I can not get the rosie server vip function to complete.  After many hours it always ends with

 

VIP Job vip put cds 81q1 prepared pdb 「№72207」 Details

 

this error :

 

Job 「№72207」has failed with the message:

JOB FAILED: Scripts failed to produce HPC jobs json file...

 

Have tried several times now, thanks for any advice

 

- Amy F

 

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AddHelixSequenceConstraints Mover2

Category: 
Design

Hello All

I want to design the interface of a two-chain complex( actually design only one of the partner)  using raf / rac design script which I have attached it here.

Is it better and more accurate to change this script in order to get and use resfile ? 

I prefer to design interface automatically without resfile (just script defines interface residues)  because I have no idea about which residues in interface should be designed or not. or what types of mutations are allowable

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File specification of binary part of silent file (especially PDB section)

Category: 
Design

Hi there,

I would like to know if somebody could share the binary file format specification of the silent file. I try to read the PDB section without any luck. Before digging through the code of extract_pdb I thought it would be faster to quickly ask how to read the binary section.

Thank you very much.

Cheers,

Max 

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protein interface design

Category: 
Design

Hello All

I want to design the interface of a two-chain complex( actually design only one of the partner)  using raf / rac design script which I have attached it here.

Is it better and more accurate to change this script in order to get and use resfile ? 

I prefer to design interface automatically without resfile (just script defines interface residues)  because I have no idea about which residues in interface should be designed or not. or what types of mutations are allowable

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How to define a theozyme from the .pdb crystal structure without ligand?

Category: 
Design

I  want to graft a coenzyme binding sites to a scaffold,  so the first thing is to define a theozyme. However, the exsiting .PDB structures  binding the coenzyme are not accessible, what I can download is only protein crystal structure without ligand. I that way, what should i do? Should i DOCK the ligand to the protein at first? could anyone explain me the procedure? Thanks a lot!

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RosettaScripts LinkResidues

Category: 
Design
Symmetry

Hey,

I want to redesign the interface of two three-fold symmetrical proteins and I thought of using RosettaScripts.
I first wanted to make it work on one three-fold symmetrical protein and then continue with the interaction, but I am stumbling on some errors.

I'm using LinkResidues, because the protein is three-fold symmetrical, so a mutation on residue a should also occur on residue b and c, thus without breaking the symmetry of those residues.

I'm using:

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Behavior of nstruct

Category: 
Design

Hi, I need your help on your experience of the number of structures generated from Rosetta by specifying nstruct:

Have you ever met a situation, for example, you specify nstruct = 100, and Rosetta generates less than 100 structures at the end of the run?

More information:

1)  I am using RosettaScripts to design a protein interface. I have specified a cutoff of SASA but I don't think it would affect the final number of structures.

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