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KeyError: 'subject-id' in antibody modelling

Submitted by bogac on Mon, 2017-03-06 02:00
Category: 
Structure prediction
Design

Dear all,

I have recently started learning Rosetta. Now I am working on antibody modelling. I have prepared my inputs, have blast and Pro-Fit working.  When I am running the antibody.py with the default preprocessing options

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Rosetta 3 - Applications

Error when running Remodel with EnzDes constraint file to extend c-terminal

Submitted by Jeffrey_Chen on Thu, 2017-01-19 06:20
Category: 
Design

hi, everybody

In my test in  running Remodel with EnzDes constraint file,

the blueprint file is:

''''
95 E .
96 F . CST1A 
97 S .
98 E L CST1B 
99 E L

#################

the cstfile is:

CST::BEGIN
  TEMPLATE::  ATOM_MAP: 1 atom_type: Nbb 
  TEMPLATE::  ATOM_MAP: 1 is_backbone
  TEMPLATE::  ATOM_MAP: 1 residue3:  ALA CYS ASP GLU PHE GLY HIS ILE LYS LEU MET ASN GLN ARG SER THR VAL TRP TYR

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Rosetta 3 - Applications

Domain insertion with Non-CAA

Submitted by mwfranklin on Mon, 2017-01-16 12:30
Category: 
Design
Loop Modeling

Hi all,

I am trying to insert a long fragment (GFPStrand) into another protein (4e1s) using Remodel. I've delete the residues that were originally in 4e1s but left a few at the end as an anchor for the domain insertion. Remodel throws an error about insertion indices being 0 if I don't leave them to anchor it. Remodel accepts the domain insertion and starts on the loop closure. It also appears to close the loop, but then throws this error with trace: 

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Rosetta 3 - Applications

Altering substrate specificity

Submitted by bp on Thu, 2016-12-22 02:45
Category: 
Design
Scoring
Enzyme Design
Small Molecules
Chemically Modified Residues

Hi all,

I'm presently working on a project to modify the substrate specificity of a DNA polymerase for non-natural nucleic acids.

I've currently been using the GreedyOptMutationMover with a ddg filter (jump across the substrate) for a 10Å shell around the active site and identified several single point mutations that have been experimentally validated to improve activity.

However, one of the problems with greedyopt is that it does not appear to screen every possible position or single point mutation within the designable region.

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Rosetta 3 - Applications

Error using FilterScan with rosettascripts

Submitted by SenyorDrew on Tue, 2016-12-13 14:29
Category: 
Design

Hi,

I'm trying to perform a residue scanning of an interface in order to identify potential mutations that can improve affinity.  I tried using the FilterScan filter:

<ROSETTASCRIPTS>

    <SCOREFXNS>
        <t14 weights="talaris2014"/>
    </SCOREFXNS>
    

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Rosetta 3 - General

Design with limited number of aminoacids at given position

Submitted by sdh_h on Sun, 2016-12-04 03:44
Category: 
Design
Constraints

Hi!

What is the easiest way to allow only a single residue type (e.g. Trp) at a given position during the design?

I use FastDesign Mover with symmetry. I thought about ReadResfile and PIKAA command, but perhaps it could be done directly from the Rosetta Script? Via task_operations=... ?

Best wishes,

Staszek

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Rosetta 3 - Applications

Ddg_monomer: implementing disulfides

Submitted by kabol on Wed, 2016-11-30 02:39
Category: 
Design

I've been using the ddg_monomer application with high resolution protocol flags and the alternative mutation file format (to obtain more than one mutation) on the constant domain of a TCR (alpha and beta chain).

 

I'm interested in 3 ddg values:

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