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Re: [ccp4bb] Calculating vertical offset of helices
 

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CCP4bb <-- 2007 <-- August 2007 <-- 06 August 2007
Previous message:
Subject: Bruker Microstar-H with Helios optics and MarDTB
From: praveen kumar praveend22 {- at -} YAHOO {- dot -} COM
Date: 2007-08-06 		Next message:
Subject: Re: Calculating vertical offset of helices
From: Jie Liu jie {- at -} TRIMER {- dot -} MED {- dot -} CORNELL {- dot -} EDU
Date: 2007-08-06


Subject: Re: Calculating vertical offset of helices
From: Edward Berry eaberry {- at -} LBL {- dot -} GOV
Date: 2007-08-06
Since Jie Liu is talking about coiled coils and heptad
repeat, I think what may be needed is the displacement
along the bundle axis. So an expression for the best
bundle axis line, and then the projection of different
C-a's onto that line to measure the difference between
them?

Ed

Eleanor Dodson wrote:

> Jie Liu wrote:
>
>>Dear CCP4ers:
>>
>>Does anyone know an existing program to calculate the lateral
>>displacement---the vertical offset, measured as a fraction of the
>>the heptad repeat---of neighboring helices in coiled coils or helix
>>bundles, either parallel or antiparallel?
>>
>>Your input is greatly appreciated.
>>
>>Have a nice weekend!
>>
>>Jie
>>
>>
>>
>
>
> Maybe I dont understand the question..
>
> If you know what you want to match to what cant you just superpose the
> Cas of helix i onto those of helix j and sort it out from that?
> Selecting the match might be tricky but you must have done that?
>
> You will need to do some geometric fiddling I guess.
> The Superpose molecule option from the GUI would give you the centre of
> mass of each segment and the direction cosines for the transformation,
> which will be those for the helix axes. I think the dot product of the
> COM onto the DCs would give you the relative displacements in As
>
> (X_com1*DC1 + Y_com1*DC2 + Z_com1*DC3) - (X_com2*DC1 + Y_com2*DC2 +
> Z_com2*DC3)
>
> Eleanor

CCP4bb navigation

CCP4bb <-- 2007 <-- August 2007 <-- 06 August 2007
Previous message:
Subject: Bruker Microstar-H with Helios optics and MarDTB
From: praveen kumar praveend22 {- at -} YAHOO {- dot -} COM
Date: 2007-08-06 		Next message:
Subject: Re: Calculating vertical offset of helices
From: Jie Liu jie {- at -} TRIMER {- dot -} MED {- dot -} CORNELL {- dot -} EDU
Date: 2007-08-06


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