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 <[EMAIL PROTECTED]> Date: Friday, November 23, 2007 12:37 Subject: Re: [ccp4bb] Summary: Symmetry of crystallographic stereographic projections? To: [email protected] > 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 \ > <<eof > 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: [EMAIL PROTECTED] > >> ******************************************************* > >> > >> > > > > > > ******************************************************* > > 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: [EMAIL PROTECTED] > > ******************************************************* > > > > > > > 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
