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*To*: Jinsong Liu <jsliu@tularik.com>*Subject*: Re: [ccp4bb]: how to align two 2-fold axis?*From*: Edward Berry <eaberry@lbl.gov>*Date*: Fri, 19 May 2000 19:07:11 -0700*CC*: "ccp4bb@dl.ac.uk" <ccp4bb@dl.ac.uk>*Organization*: Lawrence Berkeley Laboratory*References*: <3925E8A9.CEF8C823@tularik.com>*Sender*: owner-ccp4bb@dl.ac.uk

*** 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

**References**:**[ccp4bb]: how to align two 2-fold axis?***From:*Jinsong Liu <jsliu@tularik.com>

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