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Hi All,<br>
<br>
I addressed some of these questions off-list, and now I realize I've
never replied to the list. In summary:<br>
<br>
- phenix.refine always outputs two sets of 2mFo-DFc, using original
Fo and complete set with missing reflections filled in. In case of
using data massaging tools, such as STARANISO or UCLA anisotropy
correction servers, it's best to inspect both maps, because in some
cases "filled map" may be more model biased than the other one.
Note, Coot load filled map by default, so you will need to load the
other one manually.<br>
<br>
- If using massaged data, please make sure to deposit both, massaged
and original reflection data.<br>
<br>
- If using massaged data, it may be desirable to do the final
refinement run using all data.<br>
<br>
Pavel<br>
<br>
<br>
<div class="moz-cite-prefix">On 10/13/17 11:47, Ursula
Schulze-Gahmen wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CA+erM+0wL4K5s2oNENobMpHVfdQKd4yvHBwNxAxffPUC9+aRXw@mail.gmail.com">
<div dir="ltr">I have data from a crystal with anisotropic
diffraction. After scaling and merging using the webserver
staraniso, I would like to refine using phenix refine. Could you
tell me if phenixrefine will try to fill in the missing
reflections that were removed in the staraniso procedure? If so,
is there a a way to prevent this fill in? Following is the
warning message for the Staraniso server:<br>
<div><br>
<br clear="all">
We are
grateful to Andrew Leslie (MRC-LMB) for identifying a
potentially
undesirable 'feature' of CCP4/REFMAC (and possibly other
refinement
software), namely the 'fill-in' of unobserved data with <i>DF</i>calc
which makes it effectively <i>incompatible</i> with the MTZ
file output
by STARANISO. Our advice is therefore to use <b><a
target="_blank" href="http://www.globalphasing.com/buster"
moz-do-not-send="true">BUSTER</a></b> for refinement
using the downloaded MTZ file, unless the user can find a way
to disable
that feature in the alternative software.
<p>In general, any treatment of STARANISO's output data that
adds
missing reflections out to the resolution limit may result
in a very
high proportion of unobserved data compared with data that
have had a
cut-off applied according to an isotropic criterion. Where
missing
reflections have been added in this way the user should take
care to
verify that any applications used to process the data
subsequently can
handle it correctly.
</p>
<br>
</div>
<div>Ursula<br>
</div>
<div><br>
-- <br>
<div class="gmail_signature">
<div dir="ltr">Ursula Schulze-Gahmen, Ph.D.<br>
Project Scientist<br>
UC Berkeley, QB3<br>
360 Stanley Hall #3220<br>
Berkeley, CA 94720-3220<br>
(510) 643 9491<br>
</div>
</div>
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<br>
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<br>
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