[phenixbb] h_bonds restraints
Maia Cherney
chern at ualberta.ca
Sun Mar 28 09:35:05 PDT 2010
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 <chern at ualberta.ca>
> Date: Sunday, March 28, 2010 14:14
> Subject: Re: [phenixbb] h_bonds restraints
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
>
> > 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
> >
> > Pavel Afonine wrote:
> > > 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
> > the
> > > 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:
> > >> 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
> > the
> > >> coordination distances of Mg2+ (around 2A)?
> > >>
> > >> Maia
> > >>
> > >> Pavel Afonine wrote:
> > >>> Hi Maia,
> > >>>
> > >>>> I have done the things that you suggested,
> > >>>
> > >>> great!
> > >>>
> > >>>> 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
> > peaks)
> > >>> then edit the file that defines restraints for water-Mg2+
> > interactions.>>>
> > >>>> 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!
> > >>>
> > >>>> 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
> > pretty
> > >>> 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
> > project
> > >>> 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.
> > >>>
> > >>> _______________________________________________
> > >>> phenixbb mailing list
> > >>> phenixbb at phenix-online.org
> > >>> http://phenix-online.org/mailman/listinfo/phenixbb
> > >>>
> > >>>
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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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