Converting -patch replonly residues to original sequence

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    • June 26, 2017 at 8:39 pm #2680
      Anonymous

        Hi There,

        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?

        Thanks,

        Subha

         

      • June 28, 2017 at 12:36 pm #13508
        Anonymous

          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.

        • June 28, 2017 at 3:03 pm #13516
          Anonymous

            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).

          • June 28, 2017 at 5:24 pm #13517
            Anonymous

              You can also use the SimpleThreadingMover in PyRosetta or RosettaScripts:

              https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/SimpleThreadingMover

            • July 4, 2017 at 6:37 pm #13547
              Anonymous

                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.

                Subha

              • July 4, 2017 at 7:35 pm #13550
                Anonymous

                  I tried something like this. Not completely sure of what it does, 

                  Prepared an XMl file as below,

                  <ROSETTASCRIPTS>

                  <TASKOPERATIONS>

                          <ThreadSequence name=F00000012 target_sequence=”MPVRRGHVAPQNTFLDTIIRKFEGQSRKFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPRTQRRAAAQIAQALLGAEERKVEIAFYRKDGSCFLCLVDVVPVKNEDGAVIMFILNFEVVMEKDMVGSPAHDTNHRGPPTSWLAPGRAKTFRLKLPALLALTARESSVRSGGAGGAGAPGAVVVDVDLTPAAPSSESLALDEVTAMDNHVAGLGPAEERRALVGPGSPPRSAPGQLPSPRAHSLNPDASGSSCSLARTRSRESCASVRRASSADDIEAMRAGVLPPPPRHASTGAMHPLRSGLLNSTSDSDLVRYRTISKIPQITLNFVDLKGDPFLASPTSDREIIAPKIKERTHNVTEKVTQVLSLGADVLPEYKLQAPRIHRWTILHY” start_res=”1″/>

                  </TASKOPERATIONS>

                  <MOVERS>

                    <PackRotamersMover name=packrot task_operations=F00000012/>

                  </MOVERS>

                  <PROTOCOLS>

                          <Add mover=”packrot”/>

                      </PROTOCOLS>

                  </ROSETTASCRIPTS>

                  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?

                   

                  Thanks,

                  Subha

                  • July 4, 2017 at 8:00 pm #13551
                    Anonymous

                      “same structure with the correct sequence”

                      So it worked!  Unless I’m missing something, I think this is exactly what you needed?

                    • July 4, 2017 at 8:06 pm #13552
                      Anonymous

                        Yes, it worked. But just wanted to know if the way I did was correct.

                        Thanks,

                        Subha

                      • July 4, 2017 at 10:42 pm #13553
                        Anonymous

                          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.

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