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Re: [ccp4bb] Summary: Symmetry of crystallographic stereographic projections?
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
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Subject: Re: [ccp4]: Problems with ccp4bb
From: Charles Ballard c {- dot -} c {- dot -} ballard {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-11-23		Next message:
Subject: His tag on membrane protein
From: deliang deliangc {- at -} UCI {- dot -} EDU
Date: 2007-11-23


Subject: Re: Summary: Symmetry of crystallographic stereographic projections?
From: Boaz Shaanan bshaanan {- at -} BGU {- dot -} AC {- dot -} IL
Date: 2007-11-23

Doesn't POLARRFN have this option too (i.e. to print all symmetry related peaks) ? Maybe not through the gui but most likely  in command line mode.

     Boaz

----- Original Message -----
From: Eleanor Dodson
Date: Friday, November 23, 2007 12:37
Subject: Re: [ccp4bb] Summary: Symmetry of crystallographic stereographic projections?
To: CCP4BB@JISCMAIL.AC.UK

> A bit late but I didnt answer in time.
> This is one of the cases where I still wheel out ALMN to do the
> self
> rotation. It generates ALL symmetry peaks and allows you to
> select which
> axis you want to take as the polar axis. (ncode = 1 c*, ncode =
> 2 a*,
> ncode = 3 b* and so on)
> And the program output also makes an attempt to explain what it
> is doing!
>
> A script
> #!/bin/csh -f
>
> #
> almn
> hklin  /y/people/ccp4/projects/mao/maon5_all_scaleit1.mtz
> MAPOUT /y/work/ccp4//almn.map 
> <
> SELF 3 25
> RESO  10 3.5
> TITL  Jean
> CRYS file 1 orth 1 flim 1 10000000000000
> LABI FILE 1 F=F_natlo
> LIMIT 0 180 5 1    !  Beta limit 90 because
> of symmetry
> !                    If in doubt set Beta limit 180..
> FIND 5 40
> NOPR
> MAP
> END
> eof
>
>
>
> Dirk Kostrewa wrote:
> > Dear CCP4ers,
> >
> > I've asked you about symmetry in stereographic projections of
> > self-rotation functions, because I have in a monoclinic space
> group
> > with beta=97 a peak for a NCS 7-fold axis at Phi=83, Psi=90,
> > Kappa=51.4. In this self-rotation function, calculated with
> GLRF, the
> > monoclinic b-axis is oriented from south-pole to north-pole.
> Thus,
> > with Psi=90, the 7-fold lies in the a,c-plane, and I was
> wondering
> > wether it points along the c-axis by some symmetry element,
> since
> > 83=180-97. Pierre Rizkallah pointed to the fact that the self-
> rotation
> > function is calculated in Patterson space which has an
> inversion
> > centre, and Ian Tickle has pointed me to the POLARRFN
> documentation
> > that discusses some of these symmetries. From this, I can, in
> my case,
> > construct the following symmetry-equivalent positions:
> >
> > (1) Original
> Peak:                    Phi, Psi, Kappa           --->  
> > 83, 90,  51.4
> > (2) General equivalent position:     
> 180+Phi, 180-Psi, -Kappa  ---> 
> > 263, 90, -51.4
> > (3) Crystallographic Dyad

Poles:   180+Phi, Psi,
> Kappa       ---> 
> > 263, 90,  51.4
> > (4) (3) combined with
> (2):            Phi, 180-Psi, -Kappa      --->  
> > 83, 90, -51.4
> >
> > Thus, none of these combinations gives a Phi-angle of 97
> degrees.
> > However, meanwhile Liang Tong, the author of GLRF, explained
> to me,
> > that in his convention, a positive Phi angle goes from +X (=a)
> to -Z
> > (=-c*), which means that Phi=83 points really along the (-)c-
> axis
> > (thus confirming my initial hypothesis).
> >
> >              7-fold
> >               /
> >              /
> >             /
> >            b-------------- a
> >           /

> >          /

> >         / 

> >        /  

> >       c    c*
> >
> > So, many thanks to all of you who replied and helped me to
> solve this
> > puzzle!
> > I would still be interested in a textbook or paper discussing
> symmetry
> > in stereographic projections, though ...
> >
> > Best regards,
> >
> > Dirk.
> >
> > Am 22.11.2007 um 14:40 schrieb Dirk Kostrewa:
> >
> >> Dear CCP4ers,
> >>
> >> does any of you have a good reference describing the symmetry
> of
> >> crystallographic stereographic projections? There is a lot of
> >> literature describing rotational symmetry in Eulerian angular
> space,
> >> but I'm not aware of any for polar angles. In particular,
> I've
> >> calculated a self-rotation function for a crystal in space
> group C2
> >> with a monoclinic beta-angle of 97 degrees in a convention
> where Phi
> >> is the angle from the x-axis (=a-axis) and Psi is the angle
> from the
> >> monoclinic b-axis. I get a beautiful peak for a seven-fold
> rotation
> >> axis at Phi=83 degrees and Psi=90 degrees. I think that the
> >> seven-fold NCS-axis should point along the crystallographic c-
> axis,
> >> but then I would expect Phi=97 and Psi=90. Presumably, there
> must be
> >> a symmetry with the term Phi' = 180-Phi, but I would like to
> _know_
> >> it. I would be grateful for any pointer to a good reference
> >> describing symmetry in crystallographic stereographic
> projections,
> >> also for future cases.
> >>
> >> Best regards,
> >>
> >> Dirk.
> >>
> >> *******************************************************
> >> Dirk Kostrewa
> >> Gene Center, A 5.07
> >> Ludwig-Maximilians-University
> >> Feodor-Lynen-Str. 25
> >> 81377 Munich
> >> Germany
> >> Phone:     +49-89-2180-76845
> >> Fax:     +49-89-2180-76999
> >> E-mail:    kostrewa@lmb.uni-muenchen.de
> >> *******************************************************
> >>
> >>
> >
> >
> > *******************************************************
> > Dirk Kostrewa
> > Gene Center, A 5.07
> > Ludwig-Maximilians-University
> > Feodor-Lynen-Str. 25
> > 81377 Munich
> > Germany
> > Phone:     +49-89-2180-76845
> > Fax:     +49-89-2180-76999
> > E-mail:    kostrewa@lmb.uni-muenchen.de
> > *******************************************************
> >
> >
> >
>

Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Phone: 972-8-647-2220 ; Fax: 646-1710
Skype: boaz.shaanan‎
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