Maybe there is a domain shift of your protein compared to the model. If this
is the case, try to do the MP with successive domains.
2010/9/13 Paul Holland
> Hello fellow crystallographers,
>
> I am trying molecular replacement for a protein crystal dataset that has
> very high sequence similarit
On 09:50 Tue 14 Sep , Dirk Kostrewa wrote:
> I would spend some time in improving the search model, first. If there
> are more than one possible search molecules in the PDB, I usually do a
> structural alignment (ssm superposition) to get an idea about the
> flexibility of the search molecul
Two questions.
What is the resolution of your data? what is the percentage sequence
identity?
even if you are confident of C2, try using PHASER with all space groups and
searching for 2-4 monomers.
Ivan
On Mon, Sep 13, 2010 at 7:52 AM, Paul Holland wrote:
> Hello fellow crystallographers,
>
>
Dear Paul Holland,
I would spend some time in improving the search model, first. If there
are more than one possible search molecules in the PDB, I usually do a
structural alignment (ssm superposition) to get an idea about the
flexibility of the search molecules. Then I remove all parts that
Try balbes from G. Murshudov's website. It will find proper search model
and use proper truncations automatically. In addition, it will put in
your sequence.
Paul Holland wrote:
Hello fellow crystallographers,
I am trying molecular replacement for a protein crystal dataset that has very
high
Here is how I would approach this:
Use Phaser to search with monomers, or
dimers if you suspect that the biological unit is composed of dimers
and have reasonable guess at a dimer search model.
Also consider searching with N- and
C-terminal truncated search models. Sometimes a waywar
On Mon, 2010-09-13 at 15:52 +0100, Paul Holland wrote:
> that has very high sequence similarity to the search model
How high exactly?
--
"I'd jump in myself, if I weren't so good at whistling."
Julian, King of Lemurs
Does your model structure form a dimer? Maybe best to search with that
model..
eleanor
Paul Holland wrote:
Hello fellow crystallographers,
I am trying molecular replacement for a protein crystal dataset that has very
high sequence similarity to the search model with several predicted flexibl
Hello fellow crystallographers,
I am trying molecular replacement for a protein crystal dataset that has very
high sequence similarity to the search model with several predicted flexible
loop regions; however, all attempts at finding a solution have not produce very
ideal starting solutions usi
