-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Kavya,
one reason could be an incorrect script for running refmac, or a bug in refmac, or, if the distance allows, that the two peaks really are two different fully occupied atoms with a lesser anomalous signal than expected. Best, Tim On 04/19/2013 02:02 PM, Kavyashree Manjunath wrote: > Sir, > > Thank you Sir. I tried this once at the end in order to check the > refinement statistics, R, Rfree and FOM showed improvement. but I > encountered one problem. One of the a nomalous scatters which had > double occupancies (which was confirmed by anomalous peak search) > after the refinement of occupancy using "SAD data directly" it > turned out that the sum of the refined occupancies of this atom was > more than 1. Why is it so? What might have gone wrong here? > > Regards Kavya > >> Hi Kavya, >> >> In my experience, if the SAD data are good, in addition to >> helping with anomalous scatterer occupancy refinement the R >> factors can be significantly improved as well. I would give it a >> try. As far as the other options in refmac such as inclusion of >> H-L coefficients or phase, FOM, I believe that direct refinement >> against the SAD data is preferred. >> >> Philip >> >> >> On Fri, Apr 19, 2013 at 7:43 AM, Kavyashree Manjunath < >> ka...@ssl.serc.iisc.in> wrote: >> >>> Dear users, >>> >>> The native structure for a protein is available and there is a >>> ligand bound data. The crystallisation condition has anomalous >>> scattering metal ions (Cd). Both the data are scaled by >>> separating anomalous pairs. So while refining a ligand bound >>> data with a solution obtained using Molecular replacement, is >>> it recommended to refine using "SAD data directly" in refmac so >>> that the anomalous atoms can be occupancy refined? >>> >>> Thanking you Regards Kavya >>> >>> >>> -- This message has been scanned for viruses and dangerous >>> content by MailScanner, and is believed to be clean. >>> >> >> >> >> -- Philip D. Kiser, Pharm.D., Ph.D. Department of Pharmacology >> Case Western Reserve University 10900 Euclid Ave. Wood Building >> Room 317 Cleveland, OH 44106 (216) 368-8794 >> >> -- This message has been scanned for viruses and dangerous >> content by MailScanner, and is believed to be clean. >> >> > > > - -- - -- 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/ iD8DBQFRcTNHUxlJ7aRr7hoRAh2NAKCs2RCLwJfGjRUPwJrKIAhb2/ucBACg17+/ JvNU5K2lQ1jHnu/aHQ9TK94= =1zQO -----END PGP SIGNATURE-----
