Re: [ccp4bb]: how to align two 2-fold axis?

[Edward Berry <eaberry@lbl.gov>]

***  For details on how to be removed from this list visit the  ***
***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***



Jinsong Liu wrote:
> I am making a figure, in which there is a pseudo 2-fold related dimer
> and another perfect 2-fold related dimer. These two dimer should be
> connected by some linker.  I am trying to model these two dimers
> together. the problem is I can never get the two 2-fold axis exactly
> aligned. I think O is not enough to get it 100% right. So any suggestion
> about how to do that?  If I can get the axis for the pseudo 2-fold and
> then align it with the perfect two-fold (which is already known.), but
> how?
> 
> Thanks for any help.
> 
> Jinsong
> 

I'm not sure I exactly understand your question. I take it you've already
built all three monomers, and you want to align the two 2-fold axes
(with each other? with horizontal and vertical axes?) for a figure. 
Or are the two dimers from two different crystal forms?

If the problem is visuallizing the pseudo 2-fold, T. Wagner in her recent
summary described a program that will superimpose monomers to determine 
the two-fold operator, and then provide points on the rotation axis (which
could be visualized as atoms in O for precise alignment.):
----(quote)------------------------------------------------------
1. Guogang Lu referred me to his website, which, besides some other useful
stuff, hosts a program called FIT:
http://bioinfo1.mbfys.lu.se/~guoguang(/fit.html)

FIT superimposes molecules (like lots of other programs do, too) AND
writes the rotation axis out as a vector (described by two points with
orthogonal coordinates) of arbitrary length, defined by the user.
-----------------------------------------------------------------
-- 
Ed