-----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-----
