13 Oct
2005
13 Oct
'05
12:51 p.m.
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?
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Peter C. Lai
Cesium Hyperfine Enterprises
http://cowbert.2y.net/