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Usage of the TaskOperations "RestrictToCDRsAndNeighbors"

Submitted by johnnytam100 on Wed, 2019-04-10 02:58
Category: 
Design

Hi, I would like to include the TaskOperations "RestrictToCDRsAndNeighbors" in my xml file which is to design the CDR in an antibody-antigen interface.

However, I do not know what to put as options under the arguments "numbering_scheme" and "cdr_definition"

From the manual, the explanations are

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Rosetta 3 - Applications

intrensic disrodered proteins

Submitted by ac.research on Thu, 2019-04-04 07:20
Category: 
Design

Hello everyone,

I have been running several fixbb and flxbb protocols for a while now, but it seems the outcome is not very promising.

So i guess mainly the issue is with disordered structures? Whatever I RosettaDesign i always end up with decoys that have intrensic disrodered states for the majority of the residues in a structure.

this of course affect the folding simulation to determine the success of the design, as well as the crystallisability of the structure.

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Rosetta 3 - General

MSDMover error in RECON protocol

Submitted by yifeili1983 on Mon, 2019-04-01 00:44
Category: 
Design

Hi Everyone,

I'm sorry to open a new topic about the RECON multi-state design. I got the same error when I run Rosetta when I used mpi (I tried two Rosetta versions 2016.08 and 2018.09). In the error message, it said I need to pass the -run:msd_job_dist flag to make it work (I did and it still didn't work).  Here is the error I got:

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Rosetta 3 - General

Multi-state design with the error "unable to locate database file"

Submitted by yifeili1983 on Sun, 2019-03-31 18:30
Category: 
Design

Hi,

I am a new Rosetta user and learning to do the multi-state Ab design by following the RECON protocal. When I run it, I got the error said "unable to locate database file" even though I already listed the database path in .options. Could anyone help me to fix this problem? Here is the error message I got:

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Rosetta 3 - General

Specifying resfile in rosetta scripts

Submitted by johnnytam100 on Mon, 2019-03-18 02:19
Category: 
Design

Hi, I want to design a protein interface by rosetta scripts with the positions I want to mutate stated in a resfile.
However, the output generated included mutations in other positions which were not stated in the resfile. 
I wonder if there is something wrong with my scripts.
Would you mind glancing through the following (.xml, flags, resfile and the command of running)?
Thank you very much for your help!!!

 1) design_script.xml

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Rosetta 3 - Applications

Two questions on the RosettaScripts flexbb-interfacedesign.xml

Submitted by johnnytam100 on Fri, 2019-03-15 04:54
Category: 
Design

I am trying to use flexbb-interfacedesign.xml from rosetta 3.9 to do the design of a protein interface.

I have two questions:

1) The top of flexbb-interfacedesign.xml reads as the following, is there a missing open bracket before "ProteinInterfaceDesign...", as highlighted in red?
2) How does rosetta define "chain1" and "chain2", as highlighted in yellow? I have tried many times by changing either "1" or "0" and even changing the chain name in the pdb (e.g. A->B, B->A) but still I cannot control which chain to design.

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Rosetta 3 - Applications

Any backrub expert?

Submitted by johnnytam100 on Fri, 2019-03-01 01:58
Category: 
Design

Dear all,

I have just started out my work in a computational protein design lab.
The first algorithm I learned at the beginning was backrub, which I know basically could be used for flexible backbone design.
After using it for a while, I have some doubt in my mind.
Would you mind sharing your valuable experience on the following situations regarding backrub?

1) I have generated 50k structures by backrub.
After removing redundant sequences, the number of unique amino acid sequence was just 1k.

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Rosetta 3 - Applications

Clarify ProteinInterfaceDesign “randomness”

Submitted by tsztain on Wed, 2019-02-27 09:41
Category: 
Design

Hello, I am using the following protocol, modified from the design raf-rac interface demo, to design a protien protein interface. I ran 2 designs in parallel using nstruct = 1,000 and ran SequenceProfile.py to analyze and found that the results were the same for each. Therefore I wondering exactly how the sequence space is "randomly" searched to identify mutations and how likely these mutations will be to give a more favorable interface in vitro. Thanks in advance

</SCOREFXNS>

        <FILTERS>

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Rosetta 3 - General

ProteinInterfaceDesign algorithm questions

Submitted by tsztain on Mon, 2019-02-18 14:10
Category: 
Design

Hello, I am using the following protocol, modified from the design raf-rac interface demo, to design a protien protein interface. I ran 2 designs in parallel using nstruct = 1,000 and ran SequenceProfile.py to analyze and found that the results were the same for each. Therefore I wondering exactly how the sequence space is "randomly" searched to identify mutations and how likely these mutations will be to give a more favorable interface in vitro.  Thanks in advance

        </SCOREFXNS>

        <FILTERS>

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