See here for definition of polar point group: http://pd.chem.ucl.ac.uk/pdnn/symm2/polar1.htm .
SG P321 is in PG 32 which has a unique point where the axes intersect so is not polar. Note that non-centrosymmetric non-enantiomorphic PGs m, mm2, 3m, 4mm and 6mm are also polar, so it's not just rotation axes. Cheers -- Ian On 15 April 2015 at 10:44, Clemens Grimm < clemens.gr...@biozentrum.uni-wuerzburg.de> wrote: > herman.schreu...@sanofi.com wrote: > > Polar space groups have none or a single rotation axis, e.g. P1, P2x, >> P3x, P4x, P6x. Otherwise Tims argument is valid. >> > > Dear Herman, > > Is there really a general definition what a 'polar space group' is? For > example, SG P321 would have more than a single rotation axis but it would > be polar along its twofolds, wouldn't it? > > Best, > Clemens > > > In coot, I would switch on symmetry and use a fairly large box and see >> whether symmetry atoms match your built molecule. In that case, coot has >> options to write out the symmetry molecule. If not, different origins might >> have been used, or a polar shift has to be applied. In this case, you might >> try to manually superimpose your Selenium coordinate using to Rotate >> Translate Zone option. By careful only to translate, not to rotate. >> >> Best, >> Herman >> >> >> -----Ursprüngliche Nachricht----- >> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von >> Tim Gruene >> Gesendet: Mittwoch, 15. April 2015 09:58 >> An: CCP4BB@JISCMAIL.AC.UK >> Betreff: Re: [ccp4bb] Phenix: heavy atoms >> Dear Natalia, >> >> you can use Coot to generate the symmetry related molecules and see if >> the substructure matches your model. >> If your space group is polar, as in e.g. P2(1) or P2(1)2(1)2(1), your >> coordinates may float freely along the polar axis and looking the the >> symmetry related atoms would not help. I am not sure Coot has a feature to >> drag the coordinates along the polar axis. >> >> Best, >> >> Tim >> >> On 04/15/2015 05:24 AM, Natalia O wrote: >> >>> Dear All, >>> >>> >>> >>> I am new to the crystallography and I am seeking for an advice >>> considering data processing. I have a dataset with 2.8 A resolution. I >>> used hybrid substructure search program in phenix, I got the heavy >>> atom sites (selenium), and then I submitted the site to the autosol. >>> With autosol half of the residues were positioned and there are some >>> loops missing, and a part of structure was built as a chain of >>> alanines. Importantly only half of the methionines was built. Now I am >>> trying to build loops manually in Coot. I was able to build one of the >>> loops, and this loop has a methionine residue, so I wanted to check if >>> one of the heavy atom sites agrees with the self-built methionine >>> position. And here I got completely confused, because if I open a pdb >>> file containing my heavy atom sites and at the same time I open the >>> model - the coordinates, they are not placed in one asymmetric unit. I >>> expected that heavy atoms were found, and then basically “on top of >>> them” the model was built. But that’s not what I see. I am missing >>> something basic and important here and I am completely clueless. What >>> is the relation between the origin of coordinates in the file with >>> heavy atoms and the origin of coordinates of the molecular model? >>> >>> >>> >>> Thank you! >>> >>> >>> >>> Natalia >>> >>> >> - -- >> - -- >> Dr Tim Gruene >> Institut fuer anorganische Chemie >> Tammannstr. 4 >> D-37077 Goettingen >> phone: +49 (0)551 39 22149 >> >> GPG Key ID = A46BEE1A >> >> > > -------------------------------------------------- > Dr. Clemens Grimm > Institut für Biochemie > Biozentrum der Universität Würzburg > Am Hubland > D-97074 Würzburg > Germany > e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de > phone : +49 0931 31 84031 > ------------------------------------------------- >
