Don't forget you will need to adjust the contour level to see something with occupancy 0.3 - easily done with coot eleanor On 27 Jul 2012, at 11:25, Steiner, Roberto wrote:
> Or refine the occupancies with Refmac... > > Roberto > > From my iPhone > > On 27 Jul 2012, at 11:04, "Tim Gruene" <t...@shelx.uni-ac.gwdg.de> wrote: > >> -----BEGIN PGP SIGNED MESSAGE----- >> Hash: SHA1 >> >> Dear Ngo Duc Tri, >> >> I would manually set the occupancy of chain A to about 30% and chain >> B's to 70% and try again.There is density for chain A present in the >> second picture, it is just weaker. >> >> Cheers, >> Tim >> >> >> On 07/27/12 10:01, Tri Ngo wrote: >>> Dear ccp4bb, >>> >>> >>> I am working on refinement of an enzyme structure. I notice an >>> alternative conformation (gauche+ and gauche-) on both residues Phe >>> and Tyr. >>> >>> >>> Here is the image of electron density before refinement. Based on >>> the different map intensity, I am quite sure there is an >>> alternative conformation on both positions. >>> >>> >>> http://i50.tinypic.com/29zaoap.jpg >>> >>> >>> However, after running occupancy refinement by Phenix, I don't see >>> the density map at the gauche- conformation of Tyr residue. Please >>> take a look at the image 2. >>> >>> >>> http://i50.tinypic.com/anzfrn.png >>> >>> >>> So do you think the gauche- conformation of Tyr exists in this >>> structure. Should I keep it in the final model because there is no >>> positive map there? >>> >>> >>> >>> Thank you very much for your input. >>> >>> >> >> - -- >> - -- >> Dr Tim Gruene >> Institut fuer anorganische Chemie >> Tammannstr. 4 >> D-37077 Goettingen >> >> GPG Key ID = A46BEE1A >> >> -----BEGIN PGP SIGNATURE----- >> Version: GnuPG v1.4.12 (GNU/Linux) >> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ >> >> iD8DBQFQEmd7UxlJ7aRr7hoRAsy8AKCKlbHZxS+jR3JMIZbzhFQnRD13/ACeJk1D >> T7WJvAy48cOevzV6pJF4t2M= >> =lpal >> -----END PGP SIGNATURE-----
