On Wed, Apr 12, 2017, James Kress wrote:
> If I have a reference DNA oligomer like:
>
> CGCGAATTCGCG
>
> And want to do an rmsd against a trajectory of a DNA oiligomer like:
>
> GCGCTTAAGCGC
>
> Will rmsd reorient the reference (or trajectory) so that the sequences
> are properly compared, i.e. the AATT sequence in the reference is
> compared to the TTAA sequence in the trajectory where the A's and T's
> are compared against A's and T's instead of T's being compared to A's?
In spite of Jason's comments, the short answer is "no". I think you need to
clarify (for yourself) the explicit definition of a "proper comparison".
Try starting with just two nucleotides, e.g. the TpA and ApT in the very
center. (These have different conformational preferences.) You could
compare the sugar-phosphate backbones (by stripping out the bases); I can't
think of any good way to compare the base positions, even with manual
manipulation of the coordinates. (However, it's late at night here, so
maybe I'm missing something.) If you figure out what you want, the next
step is to arrange the coordinates so that each atom in the reference
conformation matches the corresponding atom in the trajectory conformation.
....dac
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Received on Wed Apr 12 2017 - 19:30:02 PDT
