Problems when inserting spin-label R1A

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    • #1938

        Dear all,

        I would like to use the spin-lable R1A (implemented as part of Rosetta EPR).

        In database/chemical/residue_type_sets/fa_standard/residue_types.txt I activated the needed lines

        ## Spin label types
        # kills my unit tests???

        Although the “kills my unit tests???” comment is not very encouraging:=)

        The problem is:

        When I try to generate a pose from sequence and create an alpha-helix, the helix is terminated at the spin label position. Here is an example IPython notebook demonstrating the problem. Does anybody have a suggestion on how to get this working?

      • #10137

          So it looks like when your structure is being created, it’s being made as three separate chains. You can see this by doing a “print pose.num_jump()” and “print pose”. You’ll see that you have a foldtree which connects 1-5 with a polymeric connection (-1), as well as 7-11, but residue 6 is connected via jumps, or non-polymeric connections.

          The source of this issue is that the pose_from_sequence() assumes that any non-canonical residue type automatically means that you need to make it a separate residue.

          The easiest way of dealing with this is probably to make a pose without your R1A residue, and then replace the residue with your new residue type. Something like the following would likely work:

          seq = ‘R’*(5 +1 + 5); print seq
          pose = r.pose_from_sequence(seq, res_type=”fa_standard”)

          r1a_pose = r.pose_from_sequence(“Z[R1A]”, res_type=”fa_standard”)
          r1a_res = r1a_pose.residue(1)

          #Replace position 6 with the residue, orienting it on the backbone
          pose.replace_residue( 6, r1a_res, True)

          # Now do your backbone manipulation, packing and scoring

          (Note that I tried manipulating the FoldTree directly, but the bond length/angles are messed up from loading, so a simple foldtree manipulation doesn’t work as well as just avoiding it in the first place.)

        • #10148

            Thank you, this works very well!

            In the same spirit I tried

            #Make mutation
            mut = r.MutateResidue(6 , 'R1A')

            Which also works and is bit less typing;) I updated the notebook with both workarounds.

            Best regards,


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