Hi Wally, We don't use an explicit C-beta positional restraint in Phenix, so there isn't any parameter you could change that would change its treatment as an outlier. Also, the C-beta deviation metric is done independent of geometry restraints, and is a static evaluation function. Much like rotamers, having an occasional outlier given very high resolution data is not a problem, and you can just ignore it if you believe your data supports the deviated chemistry. Validation metrics only reflect general guidelines for what is acceptable, and often true outliers can be some of the most interesting parts of a structure. Jeff On Fri, Aug 17, 2012 at 11:07 AM, Walter R.P. Novak wrote:

Hi,

I have a relatively high-resolution (1.1 A) structure and one threonine residue has a C-beta deviation outlier that I cannot prevent via any traditional means. I would like to try to restrain the C-beta deviation for this residue by scaling the geometry restraints for this residue, but I am not sure of how I should define the restraint for C-beta. Any suggestions are greatly appreciated.

Thanks, Wally

-- Walter R.P. Novak Assistant Professor of Chemistry Wabash College 301 W. Wabash Avenue Crawfordsville, IN 47933 Phone: 765-361-6407 Fax: 765-361-6149

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Hi, Thanks to all who replied! I refrained from going into many of the details in my initial post, and I am very thankful for al the suggestions. This residue is in an interesting location as it contacts a mutation, so perhaps we can expect some deviation. I am fairly sure Markus is on the right track (thanks for forwarding this!). I have been experimenting with an alternate conformer (there is some positive difference density, but it isn't as clear cut as many of the other cases). When I do add an alt conf, the C-beta of the offender drops from a (horrific) 0.339 A to 0.259 A, which is just outside the allowed 0.25 A. I am much more comfortable with the latter, especially given the consensus reached by Ed, Jeff and Nat. Thanks again to all. Best, Wally On Aug 17, 2012, at 12:41 PM, Nathaniel Echols wrote:

On Fri, Aug 17, 2012 at 8:35 AM, Jeff Headd wrote:

...

We don't use an explicit C-beta positional restraint in Phenix, so there isn't any parameter you could change that would change its treatment as an outlier.

Technically, it will be restrained by a combination of the bond angle and chirality restraints. While it is in fact possible to adjust the weights on these for specific atom selections, I don't recommend it, for the same reason Jeff gives.

...

Much like rotamers, having an occasional outlier given very high resolution data is not a problem, and you can just ignore it if you believe your data supports the deviated chemistry. Validation metrics only reflect general guidelines for what is acceptable, and often true outliers can be some of the most interesting parts of a structure.

Another suggestion from Markus Rudolph (whose message to the list was bounced by the server):

"is there a slight chance you have an alternate conformation of, say, 20% for this Thr? I have had this happen to me before and after inclusion of alternate conformations (based on density, of course), the Cbeta deviation went away."

which is a very good idea, and quite common at high resolution (but very easy to miss).

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Walter R.P. Novak Byron K. Trippet Assistant Professor of Chemistry Wabash College 301 W. Wabash Avenue Crawfordsville, IN 47933 Phone: 765-361-6407 Fax: 765-361-6149

Thanks Nat, I will try this immediately. Best, Wally On Aug 17, 2012, at 1:06 PM, Nathaniel Echols wrote:

On Fri, Aug 17, 2012 at 9:57 AM, Walter Novak wrote:

...

This residue is in an interesting location as it contacts a mutation, so perhaps we can expect some deviation. I am fairly sure Markus is on the right track (thanks for forwarding this!). I have been experimenting with an alternate conformer (there is some positive difference density, but it isn't as clear cut as many of the other cases).

A simple trick you could try is to reduce the occupancy of the Thr in the single-conformer model (somewhere in the 0.5-0.75 range is good) and re-calculate the maps. Sometimes this makes the difference map clear enough to show where the second conformation goes, since it isn't quite as flattened out by presence of the (full-occupancy) primary conformation.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Walter R.P. Novak Byron K. Trippet Assistant Professor of Chemistry Wabash College 301 W. Wabash Avenue Crawfordsville, IN 47933 Phone: 765-361-6407 Fax: 765-361-6149