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Re: [modeller_usage] helix alignment with gap



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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