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Pepspec Anchor Dock

Category: 
Design

Good evening, I want to use the pepspec anchor dock application and I am using the following flags file:
-ignore_unrecognized_res
-pepspec :: no_prepack_prot
-pepspec :: anchor_type PRO
-pepspec :: prep_align_prot_to input / 1CKA.nopep.pdb
-s input / 1CKA.nopep.pdb
-pepspec :: ref_pdb_list input / homol.pdblist
-restore_pre_talaris_2013_behavior
-score :: weights pre_talaris_2013_standard.wts
-pepspec :: soft_wts soft_rep.wts
-pepspec :: interface_cutoff 6
-pepspec :: n_dock_loop 1

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multi state protein design

Category: 
Design

Hello,

I have an enzyme and I want to optimize its sequence to increase its binding to one protein and decrease its binding to another protein at the same time. I recently attended Rosetta workshop and learn about multi state protein design which can be used to increase affinity of an antibody to its ensemble of antigen, but I am not sure whethe it is applicable to my case. I would appreciate any suggestions.

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Number of max allowed mutations from WT sequence

Category: 
Design

Hi folks,

I wonder if there is a way to constrain the number of maximal allowed mutations from the input sequence when doing a regular backbone-fixed design or a backbone-flexible design. For example, I only want the designed sequences away from the wild-type sequence by 5 residues at most (i.e. including 5, 4, 3, 2, and 1 mutations). Many thanks!

Kurt

 

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Error: Element 'RandomizeBBByRamaPrePro': This element is not expected.

Category: 
Design

Hi Everyone! Rosetta_scripts newby here.

I am modeling a loop with Rosetta scripts. I have managed to run mover 'SetTorsion' and get results as expected. However when I use  'RandomizeBBByRamaPrePro', I get the following error:

Error: Element 'RandomizeBBByRamaPrePro': This element is not expected.

Is perhaps this mover only on the dev version? I am using Rosetta3.9.

Thanks to all!

Best

Noelia

Post Situation: 

RosettaAntibody3 is failing with "Error: no input sequences were specified!"

Category: 
Structure prediction
Design

Hi all,

I am tryig to use RosettaAntibody3 to build a homology model for my antibody sequence. I am following the protocol workflow outlined in detail here: https://www.rosettacommons.org/docs/latest/application_documentation/antibody/antibody-protocol. The only difference is that I am modleing a VHH (heavy chain only antibody).

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how to know the precedure of solving a actural bio problem? like interface design?

Category: 
Design

hi 

im a doctorial student in the learning process of rosetta scripts

and i was to solve a problem like i got to design a protein complex A0_B0 with known structure and known complex of A1_B1 A2_B2 all Bi are homologs

i need to design a binder A0 that binds to B0

but I just dont know how

and a teacher told me that i needed to manually docking B0 to like a1

and to use fastdesign,fastrelax, to use taskops of layerdesign,limitaromachi2,PruneBuriedUnsats,and filters like BuriedUnsatHbonds

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Bug Report - Encoding issue

Category: 
Design

I had to do a hard shutdown of a workstation while remodel was running (mpiserialization, openmpi) and when it booted up, i ran remodel again. It had no issues running but checkpoint.txt has a different encoding now like this:

I have no idea why or how, but i purged and reinstalled gedit and it stays the same. I also tried vim and it doesnt display the checkpoint number properly either. It doesn't bother me at the moment, but might be worth checking out why it happens.

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How many iterations of remodel is enough?

Category: 
Design

Hello. I am wondering how many iterations is enough for remodel? Its a de-novo C-terminal extension: loop + helix of about 30 residues.

 

-in:file:s p_final.pdb
-remodel:blueprint final.blp
-remodel:num_trajectory ????
-remodel:save_top 5
-overwrite
-remodel:checkpoint
-out:file:scorefile final.sc
-ex1
-ex2
-hb_srbb 1.0
-remodel:use_pose_relax
-ignore_zero_occupancy false

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Metal Ion in symmetric design

Category: 
Design
Symmetry

I would like to run a design protocol on a protein that has, as its asymmetric unit, 2 proteins with an ion. I have done some purely AA-based symmetric design before with 2 chains controlled by separate virtual jumps and my own python-generated symdef file but I'd rather avoid doing that again :-) 

My hope was that I could put (even if suboptimal) the 2 chains and the ion in a single chain and proceed as usual in symmetric design with one chain.

Post Situation: 

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