Re: [modeller_usage] helix alignment with gap

[Guillaume LETELLIER <>]

Vivek Sharma wrote:
> Hi,
>  
> May be you would like to have a look to MODELLER's ALPHA restraints. 
> They take the helical gaps into consideration very nicely. Prevents 
> kinking and keeps the faces nicely.
>  
> Hope it helps.
Indeed it helped !
I had already try the alpha constraint, but i was applying it only to 
the gapped residues. I just realized that modeller works much better 
when applying the constraint to the whole helix length.

Thank you very much.

> Hi Guillaume,
> I'm a little confuse about your explanation...the gap is real or not?
>   
Hi Helena, and thank you for answering my unclear question.
> Probably you will need to write to those who modelled the structures
> before to ask about this gap. i think  is really unusual that someone
> could published structures that have wrong alignments...
This is right, i should probably have started here.
I was very surprised by these data, and i've checked every possible 
confusion, but there's no doubt i'm working on the same structure and 
sequences.
For me, the gap in the helix is really obvious, although it seems to 
have been ignored in previous papers.

here's the 'reference' alignment of the helix sequence found in the 
literatture :
> PLNYILLNLAVADLFMVFGGFTTTLYTSLH
> VNNYFLLSLACADLIIGTFSMNLYTTYLLM
   ** ** ** *** .            *

and here's the one I use :
> PLNYILLNLAVADLFMVFGGFTTTLYTSLH--
> VNNYFLLSLACADL--IIGTFSMNLYTTYLLM
   ** ** ** ***  : * *:  ***:


...


Guillaume

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