Dear Natalia, First a quick correction to avoid confusion: P2(1)2(1)2(1) is not polar. Polar space groups have none or a single rotation axis, e.g. P1, P2x, P3x, P4x, P6x. Otherwise Tims argument is valid.
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 -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iD8DBQFVLholUxlJ7aRr7hoRAif7AKCDPA/b+uweBgz4iBMkpkJhjtvFIgCg4tSH KZ3O8AJCQSZzn3nxrup8e/4= =SbIz -----END PGP SIGNATURE-----
