[phenixbb] Can the Update Waters routine ignore specified waters?

John Pascal jpascal at KimmelCancerCenter.org
Tue Apr 3 08:39:42 PDT 2012

Hi Pavel.

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.


On 4/3/12 11:12 AM, Pavel Afonine wrote:
> Hi John,
> no, not at the moment. Only turning water update off will leave the 
> water alone.
> Could you please explain why you would like to do this?
> Pavel
> On 4/3/12 8:01 AM, John Pascal wrote:
>> Hello All,
>> 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.
>> Best Regards,
>> John
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*John M. Pascal, PhD*
Assistant Professor
Department of Molecular Biology & Biochemistry
Kimmel Cancer Center
Thomas Jefferson University
233 South 10th Street, BLSB Room 804
Philadelphia, PA 19107

Email: John.Pascal at KimmelCancerCenter.org 
<mailto:John.Pascal at KimmelCancerCenter.org>
Phone: (215) 503-4596
Fax: (215) 923-2117
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