add missing residues into rna

[Anonymous]

Hi,

I have an rRNA pdb file (up to few hundred residues)  with missing segments of residues (from 3 to 10 residues in one missing segment; about 10 segments ) and I need to add(predict) the missing parts of structure and get a complete pdb.

1)Is it possible to do it  by PyRosetta?

2)- I installed pyrosetta and I’m trying to follow the workshops to get more familiar with rosetta more-less successful, but when I tried to load some RNApdb I got an error also  how could I use method pose_from_sequence with A, G, C, U?- Is there any tutorial or help how to do it?

3) (trying to answer 1) I hoped  I could load my pdb then insert missing parts using  pose_from_sequence and insert_pose_into_pose then set MoveMap to change only inserted residues and then use some movers something like simple de novo folding algorithm in Workshop4

I appreciate any help you can provide.

 

[Anonymous]

1) This may be possible in PyRosetta, but it looks like it hasn’t really been tried.  In addition, no API has been written, so you would basically want to read C++ code and try it in Python – not many of us know RNA enough to help.  Rhiju Das and one of the members of the lab Caleb Geneisse could help answer specific questions if you want to attempt this.  You may be able to employ some of these general methods here, but you would be in new territory: http://www.pyrosetta.org/faq#TOC-5.-Can-I-split-a-Pose-delete-residues-or-insert-residues-

2) Currently, I think you need to change the residue names.  Can you post the PDB and the error here?  Otherwise, open the pyrosetta_toolkit by typing that into a command line after sourcing SetPyRosettaEnvironment.sh and load your PDB in.  You can clean it and scan it for import into Rosetta.  It works to fix DNA and should work to fix RNA. 

3) I emailed Rhiju, and he suggested using Rosetta proper for now:

This should be possible to do the fill-in using rna_denovo_setup.py  to setup a job with the rna_denovo application:

 

https://www.rosettacommons.org/docs/latest/application_documentation/rna/rna-denovo-setup

 

 

Also check out the see also at the bottom of the page for more on RNA and Rosetta.  This will probably get you much closer to the actual structure of those regions as well as these are benchmarked and published RNA de novo modeling protocols.  

[Anonymous]

Actually, it looks like you should be able to make a pose from sequence for RNA:  http://www.pyrosetta.org/faq#TOC-6.-How-do-I-create-a-Pose-from-a-novel-sequence-

 

[Anonymous]

thank you for reply I am going to look at rosetta

[Author]

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