If you can't sequence it by examining the density then the following
likely apply:
You won't be able to tell from Rfree anyway.
You probably won't be able to get an unambiguous answer from real
space correlation.
I thought there would be more, but that's about it. Your best bet is
to carefully consider whether the identity of the peptide matters and,
if it does, devise some biochemical or biophysical experiment to
unambiguously demonstrate which peptide actually belongs in this
density. This approach will give your reviewers a warm, fuzzy feeling
when they read your paper.
James
On Sep 2, 2010, at 7:56 PM, <Rain Field> <rainfiel...@163.com> wrote:
In an isolated piece of density, I want to fit a 7AA peptide
fragment from a protein.
Only the sequence of the whole protein (200AA) is known, and I don't
know the peptide sequence.
I think it's best to try from the beginning of the whole sequence to
the end.
So is there any software or scripts which can do this automatically?
The resolution is 2.3A.
Waiting for your reply!
