Nigel, thanks for the response. I'll play around with this. BTW at some point we were talking about having these kind of qualitative descriptors of the 'tightness' implemented in reel. AFIK currently one has to edit the restraints value by hand. A simple control using radio buttons for instance for either the whole ligand or a group of restraints might do the trick. Cheers, Carsten

-----Original Message----- From: [email protected] [mailto:phenixbb- [email protected]] On Behalf Of Nigel Moriarty Sent: Friday, November 12, 2010 12:20 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Question about restraints

Carsten

I'm sure you are aware of all the things I'm going to mention but I mention them for completeness. Also, there will be a lot of differing opinions so I state mine with the coda that its by no means an absolute and others experience may suggest differing assertions. I'm sure there will be some discussion.

Your mention of over-tightening is important. The ligand is a small part of the restraints model and therefore the restraints must be viewed in light of the entire set. Making the Estimated Standard Deviations (ESD) smaller does have the result of tightening the restraints but making them more than hundred times smaller than the corresponding ESD in the protein portion is not numerically sensible.

Regarding the tightness of restraints, the ESD are in the units of the restraint. The majority of the restraints will be within the ESD of the ideal value. The variation of a restraint is dependent on the type of restraint (bonds vary less than dihedrals) and on the different coordinates being restrained (single bonds and double bonds).

Naturally, the quality of the data has an influence. You don't want to restrict the geometry if the density says something different.

Having said all that, I would suggest that for bonds the 'loose', 'medium' and 'tight' (LMT) is something like 0.05, 0.01, 0.005. For angles you could use 10., 3., 1. The remaining restraints are less likely to need adjusting but similar values could work for dihedrals and planes.

Cheers

Nigel

On Fri, Nov 12, 2010 at 6:19 AM, Schubert, Carsten [PRDUS] wrote:

...

Hi,

I was wondering what the default values for restraints in reel/elbow represent in terms of 'tightness' for lack of a better word.

I am trying to tighten up the geometry of a badly behaving ligand and want to avoid over tightening. What is the consensus out there what kind of ESDs represent a 'loose' 'medium' and 'tight' restraint for bond, angle, dihedral, planar and chiral restraints.

Thanks

        Carsten

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Hi Carsten,

yes ligand has good geometry initially, i.e. after I generate it. During

placement in coot and refinement in phenix it gets a bit distorted. In general I see these kind of problems in saturated, substituted ring systems using medium resolution < 2.0 A. The density is not clear enough to restrict the conformations of these ring systems, since it is basically enclosed in a round blob of density. So the real space refinement in coot and refinement in phenix take liberty from the freedom given in the restraints (Sorry had to paraphrase DVD here...) to fit the ligand in the ambiguous density.

We have a tool for quick real-space refinement that's geared towards making the geometry ideal in the end. I'm not sure it is useful in your situation, but may be worth a try. It works like this: mmtbx.lockit your.pdb your_refine_001_map_coeffs.mtz map.coeff_labels.f=2FOFCWT,PH2FOFCWT coordinate_refinement.run=True atom_selection='resname LIG' It works in two stages. First it attempts to maximize the real-space weight allowing for a significant (but not totally unreasonable) distortion of the geometry. This is meant to move the ligand into the density. In the second stage it scales down the "best" real-space weight and runs a number of real-space refinements until the selected atoms do not move anymore. The expected result is nearly ideal geometry. The procedure is usually very quick. If it turns out to be useful we could integrate it into phenix.refine, to be run after reciprocal-space refinement. The mmtbx.lockit command is not as user-friendly as phenix.refine. It only works with mtz files, you have to manually specify the mtz labels, and the error messages may be unhelpful. Also be sure there is a valid CRYST1 card in your pdb file. Ralf