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

Pavel Afonine pafonine at lbl.gov
Tue Apr 3 09:21:52 PDT 2012

What would be really great is to improve the algorithm so it does a 
better job, and for that I need a real example illustrating what exactly 
is not right. Providing functionality to keep waters may be good to 
have, but on the other hand it's going to be another handle for 
performing manual job, and phenix.refine has already too many handles, 
which is fine, but automation is the goal.


On 4/3/12 9:15 AM, Nathaniel Echols wrote:
> On Tue, Apr 3, 2012 at 8:50 AM, Pavel Afonine<pafonine at lbl.gov>  wrote:
>> 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.
> It is often not obvious which of these criteria need to be changed.
> Using the default settings, I always see additional peaks left over
> that to my eye look like waters, and it almost always removes waters
> that I am convinced were placed correctly.  I agree with John - it
> would be nice to be able to specify that the routine should only add
> waters and not remove any that were in the input file.  At the very
> least, it should not be removing waters that have bond restraints.
> -Nat
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