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

Pavel Afonine pafonine at lbl.gov
Tue Apr 3 08:50:43 PDT 2012

Hi John,

are these waters agree with the density? All phenix.refine is using to 
decide about whether to keep or remove a water is:
- density (mFo-DFc and 2mFo-DFc) peak height and shape;
- distance between the density peak and surrounding atoms.
The corresponding control parameters are exposed to users, so one can 
make them softer or stricter.
If phenix.refine deletes a water that only means that one or a few 
selection criteria are not fulfilled.

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.

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.


On 4/3/12 8:39 AM, John Pascal wrote:
> 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.
> Best,
> John
> 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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