- This topic has 11 replies, 3 voices, and was last updated 10 years, 5 months ago by Anonymous.
May 29, 2013 at 1:00 pm #1600Anonymous
Hi every body,
I am a new Rosetta user,
I want to model loops of my protein by preforming using fragment-based loop modelling of Rosetta,(De Novo protein-designing module).
I will use this command for modelling
But I don’t know how can I find my fragments file from database and which database,
would you please help me in this subject.
May 29, 2013 at 6:09 pm #8843Anonymous
To generate fragment files, we highly recommend you use the Robetta web server – http://robetta.bakerlab.org/ – For most uses it produces perfectly acceptable fragments at a tiny fraction of the headache.
If you really need to do something complex or custom, keep in mind that there’s an old way of picking fragments and a new way, and you’ll be better off in the long run using the new fragment picker. (https://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/dc/d10/app_fragment_picker.html)
June 3, 2013 at 4:50 pm #8855Anonymous
If you know you have a helix in the loop, and have an idea about where it is, you could look into RosettaRemodel: https://www.rosettacommons.org/manuals/archive/rosetta3.5_user_guide/d1/d8c/remodel.html
June 5, 2013 at 4:17 pm #8861Anonymous
How can I use RosettaRemodel in Rosetta 3.4, I couldn’t use it,
June 5, 2013 at 4:52 pm #8863Anonymous
But when I employ this command I did not get anything
/rosetta_tools/remodel/getBluePrintFromCoords.pl -pdbfile Loop_0911.pdb
June 5, 2013 at 5:33 pm #8865Anonymous
This is a pdb file that I generated by loop-model.
June 6, 2013 at 7:19 am #8869Anonymous
I attach my PDB file please find,
June 6, 2013 at 2:51 pm #8870Anonymous
Remodel requires renumbering from 1 as far as I know, so I used the PyRosetta Toolkit GUI ( http://www.pyrosetta.org/documentation#TOC-1.-The-PyRosetta-Toolkit ) to renumber your PDB and output a basic blueprint file you can edit in a text editor. I’ll look into what is wrong with getBluePrintFromCoords. I never had any luck with it either.
June 5, 2013 at 4:38 pm #8862Anonymous
It should be in Rosetta3.5.
June 5, 2013 at 5:22 pm #8864Anonymous
Does it give you any output at all?
One possibility is that you have a chain designation issue. By default it looks for chain “A” or chain “_”. If your PDB doesn’t have that chain (say it only has a single chain “H”), then the script won’t output anything. Either change the chain designation in the PDB, or specify the chain on the commandline:
rosetta_tools/remodel/getBluePrintFromCoords.pl -pdbfile Loop_0911.pdb -chain H > blueprint.txt
June 5, 2013 at 10:06 pm #8867Anonymous
Hmmm. Do you get something that seems reasonable for other (closely related) PDB files? Would it be possible for you to attach the PDB file that’s not working here? (You may need to change the extension to .txt for the forum software to accept it.) If the -chain option doesn’t fix things, it’s likely some edge case for that particular PDB.
June 6, 2013 at 8:15 pm #8871Anonymous
getBluePrintFromCoords.pl -pdbfile TM4_0001.txt -chain R > blueprint.txt
With the Rosetta3.5 version of getBluePrintFromCoords.pl gives me a blueprint.txt file that looks like:
1 N .
2 Y .
3 Y .
4 A .
This is pose numbered (sequential starting from one) rather than PDB numbered, — As Jared and https://www.rosettacommons.org/manuals/archive/rosetta3.5_user_guide/d1/d8c/remodel.html#Limitations indicates, you’ll need to renumber your PDB starting from 1. (Either the way Jared does, or by using the -out:file:renumber_pdb option on a Rosetta run. Using the score application with -out:pdb works well for this.)
It’s not much of a blueprint file – you’ll need to edit it according to https://www.rosettacommons.org/manuals/archive/rosetta3.5_user_guide/d1/d8c/remodel.html to do the remodeling that you want, but it’s certainly a starting point for your protocol.
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