The problem has been solved
I have a crystal structure that has 3 missing amino acid in its loop site,
How can I add the missing amino acid to the structure to remodel it.
Thanks,
Hi,
I have a strange problem regarding SymDock:
I did symmetry Rosetta previously using RosettaScrips 3.4. And it worked fine so far. Since I want to do docking on that symmetric molecule and - at least to my understanding - the Docking is not ported to Scripts for symmetry mode, I choose to use SymDock.
When I try to run it with exactly the same .pdb .sym and .params as in Scrips (which worked fine!) I get "
"...
protocols.simple_moves_symmetry.SymDockingInitialPerturbation: initialize_rigid_body_dofs: true
ERROR: unrecognized atom_type_name COO
Hi,
I preform using loop modelling base of fragment database to remodel the loops of a protein,
But when it generates several models (e.g., 10000), it changes the other part of the protein (e.g., helix conformer) too.
But I expect , only remodels the loops site not other sites.
Thanks
Hi,
I want to use rosettaremodel (i.e., run by rosetta_source/bin/remodel.macosgccrelease),
but I can not find this file in bin folder.
Thanks
Hi,
How can I replace a short helix (i.e., 8 amino acid) at a part of my protein?
Thanks
Berk
what is skip rate? (the forth column)
and when would you have a 0 at the fifth column?
thanks.
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
in:file:fullatom
-loops:input_pdb
-loops:loop_file
-loops:frag_sizes
-loops:frag_files
-loops:remodel quick_ccd
-in:file:native
-loops:ccd_closure
-loops:random_loop
-out:prefix _
-out:file:scorefile out.sc
-mute core.io.database
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.
Is it possible to relax the protein_complex i.e protein+cofactor+ligand.
If yes, how should i do it?
Thanks in advance.
-K.Prasanth
There is a amino sequence 1 to 156.
Some part of the residues which were definded by homology are between 100 and 156.
That means "I've already have a secondary structure for 100 to 156."
Finally, I want to fix between 100 and 156 residues during ab initio.
Please tell me what could I do for this work. Exactly what command do I use?
I used rosetta3.4
