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SEWING and motif file generation

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SEWING and motif file generation
#1

Hello, I am looking to use the SEWING protocol to create a new hybrid enzyme from two parent enzymes that are metalloenzymes. I am looking for more information as the documentation pages are  slim. Specifically, I wanted to use the new protocol as that takes into account ligand sites, which I figure I'll need to maintain the metal coordination residues. The first stage of creating a motif file. Base on the segment generation page (https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/composite_protocols/sewing/Segment-File-Generation) which states you need a motif file. Is there any way to automatically generate this motif file? Or am I going to have to go through each protein structure and determine all the potential motifs that may be present? 

I know in the legacy sewing protocol this is automatically done through the features reporting to a database.

Thanks

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Thu, 2018-07-12 07:28
rbjacob

I am passing this along for Sharon:

"Thank you for your interest in SEWING. The motif file required by the segment file generator is very different from the structural motifs database you are referring to--instead, it is a simple file which may consist of as little as one line that the user must create manually. The first section of the page you linked provides a description of this file including an example line. I think the confusion here is that this file specifies what type of motifs you want to include in your segment file (i.e. the elements you will want to use to build your SEWING assemblies). You do not need to provide any additional information regarding the structures present in your input structures as these will be extracted directly from the PDB files provided by the pdb_list_file option. In fact, the single example line in the "Creating a Motif File" section would be sufficient to generate a basic segment file."
 

 

Thu, 2018-07-12 10:57
smlewis

Thanks for getting back to me. I just want to make sure that the motif file is not limiting the final structure. I'll explain what I am trying to do. I am trying to combine two distantly homologous enzymes to create a new "child" version that may contain sequence and structure from both "parents". How much detail would I need to have in the motif file to make sure that all structural features are accepted?

 

Thanks

Fri, 2018-07-20 12:40
rbjacob