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Dear Sir, Thank you. I run refmac using GUI so most Probably there are two different atoms. Regards Kavya > -----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 < >>> [log in to unmask]> 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----- > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.