Yes, sorry about that. Fixed in pre-release :-/
For now, to unset them you need to click on the "No Sec Str Restraints"
radiobutton.
Richard Baxter and I discussed the specific problems in private. I
hope that he will summarize soon.
And just to be double clear, we are talking about *Regularize Zone*
here, aren't we?
You should be getting Chi-squareds less than 0.001. Are you?
Coot tells you in the console if it is applying Sec Struct Restraints
to your zone.
Paul.
On 26 Jan 2007, at 13:55, Joel Bard wrote:
> Hi-
>
> One thing I've noticed is that if you turn on secondary structure
> restraints in the Refine/Regularize Control GUI and then click OK,
> these restraints stay on even though subsequent clicking of the
> Refine/Regularize Control show the No Secondary Structure Restraints
> radio button selected. To unset the secondary structure restraints I
> click Alpha Helix Restraints and then click No Secondary Structure
> Restraints and then hit OK (though I haven't tested that this is
> necessary, merely opening the control and then saying OK with No
> Secondary Structure Restraints ticked might do it). If you regularize
> or refine a loop that lacks 2ndary structure with alpha helix
> restraints turned on you do get a mess.
>
> Not sure if that's your problem but I thought it worth mentioning...
>
> Cheers,
>
> Joel
>
>
>
> Dear list,
> Today we upgraded to v0.2 and discovered that regularization seems
> significantly different from v0.12. I greatly appreciate the ability to
> add torsion restraints, since I'm trying to use coot on a ~3.5A
> structure. But regions that regularized stably with v0.12 (matrix =
> 20.0) get thrown all around the place with v0.2 (matrix = 20.0-50.0,
> torsion restraints on or off). Thrown around to the point that side
> chains or carbonyls are ripped right off the backbone -- it's quite
> ugly. I've noticed that the situation seem to be improved if I'm either
> trying to regularize a very short poor section surrounded by a lot fo
> good stuff (2-3 residues seems the limit), or the section is already
> perfect. But when I try a weird loop that needs significant fixing (for
> example, 6 residues with 3-5 good ones on either side), regularization
> eats it alive. I recently saw a message from R. Baxter on the same
> subject, but no posts about it since the 17th. Are others having this
> problem? Is there a quick fix that we could implement?
>
> Jacob
--
http://www.ysbl.york.ac.uk/~emsley
Structural Biology Laboratory, University of York, York, YO10 5YW, UK
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