Excellent! That's exactly what the problem was. The console shows that helical restraints are still being applied with
Regularize Zone (angle Chi^2s ~1000) unless one re-clicks No Secondary Structure Restraints. Then Chi^2s are less than
0.001 and all is well with the world.
Another comment along those lines. I've noticed that it's possible to "lose" the Regularization Control (say behind
another window) and forget that it's already open. If one then opens another Control window, the first one stays open,
and changes in settings can be unpredictable. Is it possible to have Coot do some sort of cleanup, so that new windows
clean up old ones rather than opening duplicates?
Finally, while I'm thinking about it, I some times find it confusing when changing backbone torsions to have the control
separate from Dynarama (especially if I accidentally forgot to close a prev. torsion control and open a new one). It
might be more intuitive if the torsion sliders were actually attached to the bottom of the Dynarama window, with a label
of which amino acid was current being altered displayed somewhere in the Dynarama window.
Many thanks to Joel and Paul,
Jacob
> 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
> ----
> 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.
--
Jacob Corn
The Berger Lab
UC Berkeley - Molecular and Cell Biology
[log in to unmask]
phone: 510-643-8893
fax: 510-643-9290
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