On 27/02/2025 21:09, Manjula Ramu wrote:
Dear all,
I recently solved a complex structure of a protein with an
11-amino-acid phosphopeptide at 2.58 Å resolution. The asymmetric unit
contains two protein chains, and the difference map shows positive
green density (Fo-Fc positive difference density) for the peptide.
However, the density is not well-defined, making manual fitting of the
peptide challenging.
I have two key questions:
1. *How can I generate a 3D model of the 11-residue phosphopeptide?*
2. *What options are available for fitting the peptide into the
electron density?*
I would greatly appreciate any guidance or suggestions to help
complete my structure. I have attached the png file from the coot.
I somehow missed this thread.
Here for the record is what I would do:
Copy paste a triple-ala into the density
wiggle it about a bit using RSR
extend the fragment by adding a residue or two either end
convince myself that I'd got the chain direction correct (should be easy
with density for carbonyl oxygens)
(if not, then reverse fragment, or merely drag it out with low map
weight and drop it in in the other orientation)
Continue extending, adding ALAs until there was no more density to
sensibly interpret
Write out the poly ala and use coot-identify-protein which would then
give me the side-chain assignments.
then I'd mutate residue range given the above alignment.
then RSR to finish it off.
5-10 minutes.
Paul.
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