[Molvis-list] exporting _good_ h-bonds (was: export Chime h-bonds)

[Timothy Driscoll]

On Jan 3, 2006, at 11:20 a, Gale Rhodes wrote:
> Hi, Tim!
>
> On Jan 3, 2006, at 10:57 AM, Timothy Driscoll wrote:
>
>> hi Kevin,
>>
>> thanks for the clarification.  how would you define a 'high- 
>> quality' x-ray structure?  is there a generally accepted threshold  
>> for resolution or RMSD?
>
> Resolution and RMSD on bonds and angles tell you very little about  
> the quality of models. For example, a 3.0 A structure with non- 
> crystallographic averaging might be of higher quality than a 2.2 A  
> structure without it. Any parameters, like bond lengths and angles,  
> that are constrained or restrained during refinement are poor  
> indicators of quality.
>
> To become as astute judge of model quality, take Gerard Kleywegt's  
> tutorial on the subject:
>
> http://xray.bmc.uu.se/gerard/embo2001/modval/index.html
>
> I know of no better or more state-of-the-art introduction to the  
> subject. This guide helps model users understand that the pertinent  
> quality criteria depend on what you want to do with the model.
>
> Chapter 8 of my book, Crystallography Made Crystal Clear, is  
> another source of simple explanations, but Kleywegt puts you in the  
> driver's seat of some of the best vehicles for assessing quality.
>

hi Gale,

Happy New Year!  thanks for the primer; you have hit the nail on the  
head, as usuaL.  I will look at Kleywegt's url and, if I can get my  
hands on a copy, I'll check out CCC as well.

best wishes,

tim
-- 
Timothy Driscoll                                em: molvisions at mac.com
molvisions - see. grasp. learn.                 ph: 919-368-2667
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