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Hi John,<br>
<br>
are these waters agree with the density? All phenix.refine is using
to decide about whether to keep or remove a water is:<br>
- density (mFo-DFc and 2mFo-DFc) peak height and shape;<br>
- distance between the density peak and surrounding atoms.<br>
The corresponding control parameters are exposed to users, so one
can make them softer or stricter. <br>
If phenix.refine deletes a water that only means that one or a few
selection criteria are not fulfilled.<br>
<br>
You can relax water filtering criteria at the risk of adding more
spurious waters. Or you let phenix.refine do what it does, but at
the very end add missing waters and do a round of refinement without
water update so your waters are kept.<br>
<br>
I'm actually puzzled about this a bit. If you send me the PDB files
(before and after phenix.refine run, and tell which waters are
missing) then I will have a closer look. I also need the data file
(so I can run refinement myself). Please send files off-list, to my
email.<br>
<br>
Pavel<br>
<br>
On 4/3/12 8:39 AM, John Pascal wrote:
<blockquote cite="mid:4F7B19BE.6050200@mail.jci.tju.edu" type="cite">
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Hi Pavel.<br>
<br>
The waters around the metals agree quite well with previously
determined structures, and some of the waters are included in the
metal.edits file describing the expected metal-water distances.
These same waters are sometimes removed during the routine, and
their residue number is given to a different water residue that
has been selected at a different location in the structure. So in
subsequent rounds using the same metal.edits file introduces a
model distance that is no where near the distance defined in the
.edits file, and causes program termination. I can of course
remedy this, but my feeling is that the metal sites should be
handled carefully by me, and then left alone as the rest of the
structure is tested for additional waters. Thanks.<br>
<br>
Best,<br>
John<br>
<br>
On 4/3/12 11:12 AM, Pavel Afonine wrote:
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Hi John,<br>
<br>
no, not at the moment. Only turning water update off will leave
the water alone.<br>
<br>
Could you please explain why you would like to do this?<br>
<br>
Pavel<br>
<br>
On 4/3/12 8:01 AM, John Pascal wrote:
<blockquote cite="mid:4F7B10B5.2070206@mail.jci.tju.edu"
type="cite">
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Hello All,<br>
<br>
While using Update Waters in the phenix GUI, several waters
that have been defined around a metal binding site are
removed. I am happy with the placement of these waters - can
I specify somewhere that Update Waters should leave them
alone? and that their positions, etc. are still refined
during the run? Thanks.<br>
<br>
Best Regards,<br>
John<br>
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<br>
<div class="moz-signature">-- <br>
<b>John M. Pascal, PhD</b><br>
Assistant Professor<br>
Department of Molecular Biology & Biochemistry<br>
Kimmel Cancer Center<br>
Thomas Jefferson University<br>
233 South 10th Street, BLSB Room 804<br>
Philadelphia, PA 19107<br>
<br>
Email: <a moz-do-not-send="true"
href="mailto:John.Pascal@KimmelCancerCenter.org">John.Pascal@KimmelCancerCenter.org</a><br>
Phone: (215) 503-4596<br>
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