[phenixbb] Restraints on water molecules

Pavel Afonine PAfonine at lbl.gov
Sun Mar 8 22:02:02 PDT 2009


Hi Engin,

thanks for understanding! I will think some more of what we can do in 
future to facilitate the issues like this. My hope is that if I add a 
map CC as an additional filtering criterion then it might partially 
resolve this issue (which I will do soon) but of course there is no 
guarantee ...

Pavel.


On 3/8/09 9:52 PM, Engin Ozkan wrote:
> Thanks Pavel, you are as prompt and helpful as always.
>
> I agree that fixing waters sounds like a very, very bad idea.  I am only 
> thinking of adding restraints for waters coordinating metals (with 
> appropriate sigma), where water-metal distance can easily get down to 2 
> A (A possibly bigger issue that I haven't given much thought to might be 
> that such a water ends up being very close  (~3.2-3.5 A) to four more 
> metal-coordinating oxygens; that may look impossible from a hydrogen 
> bonding water point-of-view).  Playing with water selection criteria 
> would have global effects, quite significant in a structure with 800 
> water molecules (as of yet). I think I'll stick with what I was doing, 
> or maybe add a last ordered_solvent=False to the refinement at the end.
>
> Engin
>
> Pavel Afonine wrote:
>   
>> Hi Engin,
>>
>> Sorry for the inconvenience...
>>
>> Water molecules are treated slightly different in phenix.refine than the 
>> other atoms. For example, you cannot preserve a specific water molecule: 
>> it it falls outside a selection criterion (distances, peak heights, 
>> etc...), than it will be removed anyway.
>>
>> The only way to preserve your favorite waters is:
>>
>> - either turn water picking off: ordered_solvent=false
>> - or do what you did: rename it somehow so phenix.refine "don't think" 
>> that it is water.
>>
>> None of the above options sound attractive to me but this is how it is 
>> right now.
>>
>> There are pros and cons for this approach and there was a discussion 
>> about it a few months ago. In the end I agreed that we need an option to 
>> preserve "user's favorite" waters.  It is in my list, implementing it 
>> may take some time - it's not very straightforward. In general, the 
>> whole water picking procedure in phenix.refine needs some review (for 
>> example, use map CC as additional criterion, etc...). Although I still 
>> don't like the idea for fixing waters: what if the user fixes a water 
>> that later on in refinement proves to be noise peak and so its B-factor 
>> jumps sky high, it moves somewhere, etc, but phenix.refine will not be 
>> able to remove it since the user ordered to not do so... Could you 
>> rather play with selection criteria so your waters stay?
>>
>> Pavel.
>>
>>
>> On 3/8/09 4:02 PM, Engin Ozkan wrote:
>>   
>>     
>>> Are restraints on water molecules overwritten on successive cycles of 
>>> refinement where ordered solvent is on?  I seem to lose my distance 
>>> restraints between specific waters and metal, unless I name my water 
>>> molecules something else (and supply phenix with a cif for that name 
>>> which is identical to water inside). The distance restraints also seem 
>>> to be in effect for all cycles if ordered_solvent is off.
>>> I am also trying to make sure water numbers don't change during solvent 
>>> picking/deleting.
>>>
>>> Engin
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>>>   
>>>     
>>>       
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