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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