Hi,
If I understand your problem correctly you need to change the template
instead of the target sequence since you want to reverse the order of the
residues in the structure, essentially creating a new fold (mirror image?).
A quick solution would be to use only C-alphas coordinates from the original
template and reverse their order in the PDB file. You start with coordinates
for the c-term H C-alpha, which now becomes an n-term H in the new template
and end with the coordinates for the n-term E C-alpha, which now becomes a
c-term E. This step is basically just text editing (remember to renumber the
residues and reverse the template sequence in the alignment). Now you can
use this new C-alpha template to model your target sequence. I guess there
is no way around loosing the rest of the structure (backbone and sidechain
atoms) since anyway their positions are not likely to be compatible with the
"new fold". Not sure if this is what you want.
Best,
Roberto
--
Roberto Sanchez, Assistant Professor
Structural Biology Program, Department of Physiology & Biophysics
Mount Sinai School of Medicine
Box 1677, 1425 Madison Avenue, New York, NY 10029
phone +1 (212) 659 8648, fax +1 (212) 849 2456 http://sanchezlab.org/
> -----Original Message-----
> From: [mailto:modeller_usage-
> ] On Behalf Of Peter C. Lai
> Sent: Thursday, October 13, 2005 3:52 PM
> To:
> Subject: [modeller_usage] howto reverse polarity
>
> 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/
>
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