[phenixbb] Restraints on water molecules
PAfonine at lbl.gov
Sun Mar 8 22:02:02 PDT 2009
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
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.
> 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?
>> 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
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>> phenixbb mailing list
>> phenixbb at phenix-online.org
> phenixbb mailing list
> phenixbb at phenix-online.org
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the phenixbb