I am trying to model a protein with disordered regions and found a paper that mentioned using -replonly_residues will be helpful in such case. I have run the simulation and when I checked the output structures , all of the replonly residues are mapped as 'GLY'. Is there a way to re-map them to the original sequence in the PDB coordinate file?
The non-automatic way to do it is to write a resfile and do it with the fixbb app - basically do protein design to a prespecified sequence. I'll ask if there's a faster way to do threading.
https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/TaskOperations/taskoperations_pages/ThreadSequenceOperation has been suggested as a workaround (this can be written into a simple RosettaScript - just run PackRotamersMover with this TaskOperation).
You can also use the SimpleThreadingMover in PyRosetta or RosettaScripts:
Thanks for the reply. Could somebody help me with a sample xml file for doing this. Going through the links, it is not clear which are the ones that are necessary and how to define them.
Thanks very much for the support.
I tried something like this. Not completely sure of what it does,
Prepared an XMl file as below,
<ThreadSequence name=F00000012 target_sequence="MPVRRGHVAPQNTFLDTIIRKFEGQSRKFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPRTQRRAAAQIAQALLGAEERKVEIAFYRKDGSCFLCLVDVVPVKNEDGAVIMFILNFEVVMEKDMVGSPAHDTNHRGPPTSWLAPGRAKTFRLKLPALLALTARESSVRSGGAGGAGAPGAVVVDVDLTPAAPSSESLALDEVTAMDNHVAGLGPAEERRALVGPGSPPRSAPGQLPSPRAHSLNPDASGSSCSLARTRSRESCASVRRASSADDIEAMRAGVLPPPPRHASTGAMHPLRSGLLNSTSDSDLVRYRTISKIPQITLNFVDLKGDPFLASPTSDREIIAPKIKERTHNVTEKVTQVLSLGADVLPEYKLQAPRIHRWTILHY" start_res="1"/>
<PackRotamersMover name=packrot task_operations=F00000012/>
and ran it with
mpiexec -n 12 $ROSETTA/bin/rosetta_scripts.mpi.linuxgccrelease -database $ROSETTA/database -parser:protocol ./packrot.xml -in:file:s ./F_00000012.pdb -out:pdb -seed_offset 10
And got the same structure with the correct sequence. Is this the correct way of doing this?
"same structure with the correct sequence"
So it worked! Unless I'm missing something, I think this is exactly what you needed?
Yes, it worked. But just wanted to know if the way I did was correct.
Your script is what I was suggesting to you. It works, so it's correct. There isn't a higher definition of "correct" here than "it works", I think.