Hi CJ--
>
> I have a question regarding refining against RDCs in XPLOR-NIH. The software
> has been running error-free for me, but I'm noticing the orientation tensor
> pseudoatom is not being placed where I'm expecting it to go. I'm refining an
> axially symmetric 11-mer and fixing the rhombicity at 0 while letting Da vary.
> I'm expecting the tensor pseudoatom to be in the center of the protein with
> the z-component in the same direction as the axis of symmetry. I get this
> result when calculating RDC values using the Bax group's DC server tool.
> However, the output files generated after an XPLOR refinement have the
> pseudoatom placed outside of the protein ring.
>
> Is there a function that lets me have some control over where the pseudoatom
> goes? If not, how can I configure my code and/or input files to get the tensor
> where it should be going? I've experimented with the alignTensorToZ function,
> but still get the same result.
The absolute position of those pseudo atoms is immaterial to the
calculation of the RDC- the orientation of these atoms relative to the
protein is, of course, significant. If you would like to center the OO
pseudo atoms e.g. the origin, you might try
OOpos=AtomSel("resname ANI and name OO")[0].pos()
from atomSelAction import Translate
AtomSel("resname ANI").apply( Translate( -OOpos ) )
at the end of the calcOneStructure function.
[This assumes a single aligning medium.]
I hope this helps--
Charles
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