I am using a structure-based alignment, and I want to model a sequence
based on a template, but I want to model my sequence with inverted polarity
to the template. That is, I want to model starting from the C-term of the
template backwards to its N-term. If I invert my sequence in the alignment,
the result is structurally sound, but now they are obviously bonded
incorrectly.
For example, my template is:
>P1;1u19
structureX:1u19.stripped:33:A:65:A: rhodopsin: Bovine: 2.20: 0.200
EPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQH*
and my sequence is (n)-FVFKIVIVIGILPLLNLVGVVKLI-(coo) but I want the F
positioned near the H end and the ile positioned near the glu in the template
etc. How would I go about doing this?
--
Peter C. Lai
Cesium Hyperfine Enterprises
http://cowbert.2y.net/