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Hi Todd,<br>
<br>
in general you can refine any selected part of your model using any
combination of refinement strategies. The are a few exceptions, and
Cartesian SA is one of them: it is applied to all atoms. It is in the
list of things to address.<br>
<br>
SA refinement is good at early stages of refinement to correct gross
errors, but it may do
more harm than good for a relatively good structure.<br>
<br>
I think in your case, Rwork/Rfree = 0.2478/0.2849, you can safely
continue without doing SA. Although what you can try is the new feature
- the local real-space refinement ("fix_rotamers=true" option). This is
very powerful tool for automatic correction of side chains (you need to
have one of the latest PHENIX versions for this). More details here:<br>
<br>
<a class="moz-txt-link-freetext"
href="http://cci.lbl.gov/%7Eafonine/rsr.pdf">http://cci.lbl.gov/~afonine/rsr.pdf</a>
<br>
<br>
Regarding the B-factors: yes, this seems logical - if some U atoms gets
displaces out of their density peaks then the refinement will try to
smear them out so they do not contribute to the Fcalc, and enormous
increased B-factors is the way to do this. If you allow occupancy
refinement, their occupancies will probably refine to zero or close.<br>
<br>
I'm not sure I understood this: are these atoms still moving out of
density even if you do refinement without using SA? If this is the case
then I do not know why this happens and I would really like to know. If
you send me the data and model I might be able to figure this out.<br>
<br>
Let me now if you have any questions or problems!<br>
<br>
Pavel.<br>
<br>
<br>
On 4/7/10 1:47 PM, Green, Todd wrote:
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<p><font size="2">Hello all,<br>
<br>
I am refining a structure which contains several uranyl sites. I know
the atoms should be there based on peaks in anomalous difference
fourier maps, peak heights are greater than 10 sigma. Likewise we have
solved the apo-structure before with the same heavy atoms. If I perform
simulated annealing, the heteroatoms get pushed as far as 8 angstroms
away. The Asp(s) and Glu residues that coordinate the uranyl ion then
just move into the region of the map where the U has vacated. The
resulting fofc difference map has a huge peak(>11 sigma) where the U
should be. I noticed that if I inflate the starting b-factor for the U,
the positions will stay put(relatively). What is the best thing to do
here? Can I fix their positions, so that this does not happen? How do I
do it? I found a post in the archives that says i can use:
refine.sites.individual="not element U". Will this work for the SA? I
know it works during refinement. Anyway, the data is to 3 angstrom.
Here is the result from some SA runs:<br>
<br>
following simulated annealing:<br>
no u, starting b-factor for all atoms 20:<br>
Final R-work = 0.2502, R-free = 0.2899<br>
with u starting b-factor 20:<br>
Final R-work = 0.2771, R-free = 0.3094<br>
with u inflated starting b-factor for U:<br>
Final R-work = 0.2682, R-free = 0.2983<br>
After further manual rebuilding and TLS refinement(with u):<br>
Final R-work = 0.2478, R-free = 0.2849<br>
<br>
<br>
Also, during further refinement(if I reposition the U(s)), some of the
U(s) still get displaced and the b-factors get extremely high, some as
high as 500. I think this is due to them being displaced though. Other
datasets which I have refined with phenix don't exhibit this behavior.
Could it have something to do with NCS restraints on the protein?<br>
<br>
any suggests?<br>
<br>
Thanks in advance-<br>
Todd</font>
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