Quick navigation:        Home   |    Site Map   ||    References   |    Biography   ||    Copyright   |    Other copyright   |    Contact us   |   
Protein structure
 

Re: [ccp4bb] Calculating vertical offset of helices
 

Basic tutorials: 		 
 

CCP4bb navigation

CCP4bb <-- 2007 <-- August 2007 <-- 06 August 2007
Previous message:
Subject: Hg rippled summary
From: Klemens Wild Klemens {- dot -} Wild {- at -} BZH {- dot -} UNI-HEIDELBERG {- dot -} DE
Date: 2007-08-06 		Next message:
Subject: Dnase activity in E. coli expressed his tag proteins
From: Narayanan Ramasubbu ramasun1 {- at -} UMDNJ {- dot -} EDU
Date: 2007-08-06


Subject: Re: Calculating vertical offset of helices
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-08-06
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: Hg rippled summary
From: Klemens Wild Klemens {- dot -} Wild {- at -} BZH {- dot -} UNI-HEIDELBERG {- dot -} DE
Date: 2007-08-06 		Next message:
Subject: Dnase activity in E. coli expressed his tag proteins
From: Narayanan Ramasubbu ramasun1 {- at -} UMDNJ {- dot -} EDU
Date: 2007-08-06


ProteinCrystallography.org: Copyright 2006-2007 by Quid United Ltd