Hi Boaz, The problem is with the distance between 2 waters and not the Mg-water distance. These 2 waters belong to the Mg coordination, still they should be at a h_b distance from one another. I got around this problem by setting my custom restraints, but I think the program should take care of this. Maia Boaz Shaanan wrote:

Hi Maia,

Can I make two comments concerning the distance restraints that you're struggling with: 1) I don't know the resolution your structure, nor do I know the way Phenix treats the distance restraints internally, but I guess it's similar to the way it is in CNS. That is, there is a value for the restaint (2.1-2.2 A in your case) and there should be a number for the tolerance of that distance (or its s.d.) which the user can decide on, depending on the resolution. It is possible that Phenix is clever enough to figure out this tolerance from the resolution and the complete set of restraints, I'm not sure.

2) I wouldn't worry too much about the validation (as in fact Pavel has alluded to). If your water molecules in the Mg+2 coordination sphere "insist" on being closer to the metal than you expect, despite all your efforts, then this is it. The RCSBpeople and validation process should know about standard and deviation and resolution. In the worst case your deposited structure will have a comment/remark put in your deposited PDB saying perhaps that the Mg-water distances are shorter by that much from the norm.

That's my 2p worth thought.

Cheers,

Boaz

----- Original Message ----- From: Maia Cherney Date: Sunday, March 28, 2010 14:14 Subject: Re: [phenixbb] h_bonds restraints To: PHENIX user mailing list

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Hi Pavel,

I have waters that are part of the Mg2+ coordination. They should be at ~2.1A from Mg2+. At the same time, they should be at a hydrogen- bonding distance from each other (minimum 2.2A otherwise the validation at the PDB complains). The two waters after refinement without restraints had closer (2.12A) distance between them, so I managed to restrain the distance to 2.23A using pdb_interpretation. But my question was, should not the refinement automatically restrain close distances between any atoms, including waters? (By the way, I picked them manually).

Maia

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Hi Maia,

I'm not sure I understand the question. If you have that specific water in your structure already (and you run phenix.refine with "ordered_solvent=false"), then changing the h_bond_min_mac or h_bond_min_sol will not change anything since these parameters are used in water update.

However, if you are at the stage of water picking and the distance between Mg2+ and prospective water peak is 2.2A then the water will be placed there (providing that the corresponding peak satisfies

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other criteria).

Could you please explain what exactly the problem is, and then I will try my best to give you the solution?

Thanks! Pavel.

On 3/27/10 5:23 PM, Maia Cherney wrote:

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Hi Pavel, what is h_bond_min_mac and h_bond_min_sol.

which one should I change to 2.2 so that it will not affect

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coordination distances of Mg2+ (around 2A)?

Maia

Pavel Afonine wrote:

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Hi Maia,

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I have done the things that you suggested,

great!

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and I have all the restraints for the Mg2+ and I see those 2 waters, but they are at 2.12A distance.

Are these two waters located in the centers of corresponding density peaks? If this is the case then I don't see the subject of your worries. If this is not the case (these waters are off the

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then edit the file that defines restraints for water-Mg2+ interactions.>>>

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I think there should be some general restraints that should keep h_bonds at least at > 2.2A.

Yes. You wrote it yourself in your previous email:

h_bond_min_mac = 1.8 h_bond_min_sol = 1.8 h_bond_max = 3.2

Just change the values to what you like!

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That is why I asked you about those defaults (1.8A etc). Why are they at 1.8A? Should not they be at least at 2.2A?

Honestly, I don't remember why I put these values (this is

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old code in phenix.refine that I wrote several years ago). All I recall is that I had a reason for this. I probably need to run through the whole PDB and see how the density peaks (actual, residual, omit-residual) are distributed w.r.t. macromolecule, and write it somewhere for the future reference. This could be a

Pavel Afonine wrote: the the peaks) pretty project

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for a few weeks, but it will definitely yield a rock-solid conclusion about "good" distances. Meanwhile feel free to edit the available parameters.

By the way, this is what CNS is using:

{* minimum distance between water and any atom *} {===>} min=2.6; {* maximum distance between water and any atom *} {===>} max=4.0;

{* minimum hydrogen bonding distance between water and O or N *} {===>} hmin=2.0; {* maximum hydrogen bonding distance between water and O or N *} {===>} hmax=3.2;

Pavel.

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Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan

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