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Re: [modeller_usage] missing residues



On 5/3/12 3:29 AM, Mary Varughese wrote:
I have a dimer protein with missing residues in both subunits.

I have the target sequence, the original protein pdb with missing gaps
*(a.pdb* resolution 3.58 Xray structure)and another pdb of the same
protein with missing residues included (*b.pdb* resolution 3.5 electron
diffraction)

So i have to add missing residues with b.pdb as the template and rest of
the protein exact to a.pdb)

Yes, that should be fairly straightforward - simply use both templates in modeling, and align the model with a.pdb or b.pdb accordingly. If possible, try to overlap the regions a little so that Modeller can figure out the conformation of the missing regions.

Also can i add missing residues in both A and B units simultaneously.

Sure, that's no problem. Your alignment might look something like:

>P1;a
...
AAAAAAAAAA------AAAAAAAAAA/AAAAAAAAAA------AAAAAAAAAA*
>P1;b
...
--------BBBBBBBBBB--------/--------BBBBBBBBBB--------*
>P1;model
...
MMMMMMMMMMMMMMMMMMMMMMMMMM/MMMMMMMMMMMMMMMMMMMMMMMMMM*

(This assumes that you've edited b.pdb to only include the regions in the alignment above.)

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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