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Structure prediction

changing the chain id

Submitted by aneamtu on Tue, 2018-01-09 00:08
Category: 
Structure prediction

Hi!

 

I need to change the chain ids for 10000 pdb structures generated by the relax protocol. I have 2 chains A and B in each protein (antibody) and I want to change them yo H and L (as antibody_H3 seems to request that the heavy chain of the antibody should be name d'H').  I saw in older posts that there should be an utility:

changeChain.pl - change the chain ID of a specified chain from a pdb file.

but I cannot find it the Rosetta source.

Any suggestions?

Many thanks,

Andrei

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Rosetta 3 - General

Can I thread a two chained structure in RosettaCM?

Submitted by ahmadkhalifa on Mon, 2018-01-08 09:41
Category: 
Structure prediction

Most Rosetta CM tutorials show a one chain example for threading. If my structure has two chains, is it possible to align and thread my two chained sequence and template in a one run.

What should the grishin alignment format for the two chains look like?

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Rosetta 3 - General

cyclization_type flag in simple_cycpep_predict

Submitted by Florent Langenfeld on Thu, 2018-01-04 09:22
Category: 
Structure prediction
Design
Constraints

Dear Rosetta users or developers,

 

I'm trying to model small, cyclic peptides with the simple_cycpep_predict routine. While I explicitely asked for a terminal disulfide cyclization (using the flag -cyclic_peptide:cyclization_type terminal_disulfide), the output models are cyclized with a mainchain bond (the default n_to_c_amide_bond).

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Rosetta 3 - Applications

H3 modelling scoring function

Submitted by aneamtu on Wed, 2017-12-27 23:10
Category: 
Structure prediction

Dear all,

Let's suppose we have the following situation:

I have an antibody structure generated by the 'antibody.linuxgccrelease' (i.e. no H3 optimization yet, just grafting)

Is it possible to score it in a similar fashion as the 'antibody_H3.linuxgccrelease' application does? I mean to score it without, H3 optimization whatsoever?

I saw that in the scoring file of a H3 optimization run we can find different terms than in a normal Talaris2014 relaxing/scoring:

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Rosetta 3 - General

Comparative modeling using a two chained template for a one chain structure

Submitted by ahmadkhalifa on Mon, 2017-12-18 11:00
Category: 
Structure prediction

Hello,

I'm still a bit new to Rosetta. I'm trying to follow the tutorial for comparative modeling here: https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/RosettaCM. 

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Rosetta 3 - Applications

comparative modelling of a complex

Submitted by sdh_h on Sun, 2017-12-17 06:07
Category: 
Structure prediction
Docking
Constraints

Hello All,

I have a protein sequence that consists of two domains: A and B. The two domains presumably interact and there are some residue pairs that can be used as constraints. However, I don't know whether these domains interact within a single protein (A-B) or a dimer (A-B', B-A'). Given the fact that both A and B have many good templates in PDB, I thought that Rosetta comparative modeling protocol could be used to investigate these two scenarios. I would appreciate suggestions on how to set up such an analysis.

Best wishes,

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Rosetta 3 - Applications

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