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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:
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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>
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<br>
<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 href="mailto:John.Pascal@KimmelCancerCenter.org">John.Pascal@KimmelCancerCenter.org</a><br>
Phone: (215) 503-4596<br>
Fax: (215) 923-2117<br>
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