How do you suggest superimposing the residues? What program would you
suggest using? How do I replace the two residues with the longer
regular helix. I had thought of this but didn't know how to do it.
Kara Di Giorgio
On Jul 25, 2005, at 2:39 PM, David A. Case wrote:
> On Sun, Jul 24, 2005, Kara Di Giorgio wrote:
>
>> I have a piece of DNA from the protein data base and I'd like to
>> extend
>> the ends by two residues. Does anyone have any idea how to easily do
>> this?
>>
>
> Build a regular helix with the sequence you want, that partially
> overlaps
> the two residues in the database file. Then superimpose the atoms of
> the two
> residues in the database file with those of the regular helix. That
> will
> orient the regular helix in the right way. Then you can replace the
> two
> residues in the database file with the (longer) regular helix. You
> will
> probably need some minimization to make sure that there is no strain
> at the
> interface region.
>
> ...good luck....dac
>
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Received on Tue Jul 26 2005 - 03:53:00 PDT
