Re: [ccp4bb] question about composite omit map

[Ed Pozharski]

On Wed, 2011-03-09 at 02:25 -0500, Kyuwon Baek wrote:
> Is there any resolution limit for the composite omit map?

Probably not and I would think that it is more useful at low resolution
where model bias is stronger.  But shouldn't you be talking about
simulated annealing as a bias removal tool rather than composite omit
map?  As far as maps go, solvent flattening may be even better option.

As a general comment, outcome of almost any refinement trick may vary
from dataset to dataset.  There are general tendencies, but the best way
to answer your questions is perhaps to calculate the map and look at the
result.

-- 
"I'd jump in myself, if I weren't so good at whistling."
   Julian, King of Lemurs

[ccp4bb] question about composite omit map

[Kyuwon Baek]

Dear all,

I wonder if there is anyone who ever tried composite omit map with low
resolution data.

Is there any resolution limit for the composite omit map? or any criteria
could help deciding the practicability, like quality of data, map or
resolution?

I have ~3.7A resolution data and MR solution (~40% Rfree), obtained from the
two partial structures, reported before with 2.2A and 1.8A respectively.
After extensive iterative refinement the Rfree is close to ~30% and each
subunits shows noticeable conformational difference within complex.

I am considering the composite omit map to test whether this difference
comes is real or comes from model bias during refinement.
Do you think it's a reasonable idea with this resolution?
If not, any suggestion for this purpose?

Thanks in advance for sharing your valuable time.


  Kyuwon Baek, Ph.D