[phenixbb] modify the helices

Vellieux Frederic Frederic.Vellieux at ibs.fr
Mon Jul 19 04:27:54 PDT 2010

Hi there,

At low resolution, the quality of the electron density can lead you to 
introducing errors in the modeling process. In particular, the density 
for the side chains degrades (and below a certain resolution, helices 
appear only as filled tubes - all detail has gone). I don't know what 
low resolution you are talking (writing) about, but I'd certainly try to 
position an "ideal" alpha-helix using a few large side chains (if you 
are lucky to have any in that helix), refine using secondary structure 
(helical) restraints, and see if it makes sense afterwards.

And low resolution refinement is not an easy process, as you will find out.


xinghua qin wrote:
> hi everyone:
>    Thanks for all the response!
>    what I said last time may be chinglish and lead to some 
> misunderstanding, the word I said fix a helix means that the model 
> quality of the helix is not very good, I want to modify it manually.It 
> is so hard to do this in  low resolution.I modified the helix 
> according to the electron density map, after refinement, large red 
> areas appear in the difference map. That made me crazy!
>   Are there any suggestions or any reviews about this point?
>   I am new beginner to structural biology,  any suggestions are welcomed !
> Best regards
> Xinghua Qin

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