Hi, It's possible to do this in Phaser, but two features are missing from the AutoSol GUI: using a partial model derived from density, and searching for a cluster compound. I think the Phaser-EP GUI can search for a cluster compound, but that GUI also lacks the ability to use a partial model derived from density. We'll have to add that feature! In the meantime, you can run the job using a shell script like this one: #! /bin/csh phenix.phaser << eof > MRSAD_density_cluster.log MODE EP_AUTO ROOT MRSAD_density_cluster HKLIN 1hkx.mtz CRYSTAL TaBr DATA TaBr LABIN F+=FOBS(+) SIG+=SIGFOBS(+) F-=FOBS(-) SIG-=SIGFOBS(-) COMPOSITION PROTEIN SEQUENCE 1hkx.fa NUM 1 WAVELENGTH 1.2543 PARTIAL HKLIN 1hkx_with_2f86.1.mtz IDENT 53.0 # Output MTZ file from MR search with density as a model LLGCOMPLETE COMPLETE ON SCATTERER TX # Search for Ta6Br12 cluster, which is handled specially in Phaser END eof This is an example where I used two copies of a heptamer from 2f86 to solve 1hkx, which contains a Ta6Br12 cluster. The MTZ file written after the molecular replacement solution contains FC and PHIC for the structure factors calculated from the model, whether the original model comes from electron density or an atomic model. The PARTIAL HKLIN command provides that MTZ file, and the FC and PHIC columns are used by default. If you give the wavelength, you shouldn't have to worry about f' and f" because Phaser looks up reasonable values from a table. If you have any trouble, please get in touch! Also, you might want to try just searching for individual Ta atoms, in case that gives a sensible result. Best wishes, Randy Read On 1 Oct 2013, at 06:02, LISA wrote:

Hi All,

If we have partial model we can run MR_SAD by adding a single new keyword to my AutoSol run: input_partpdb_file=MR.pdb

But I only have a mtz file not a pdb file in the molecular replacement result with EM map as the model. How can I combine the EM result with SAD to improve the density? I have Ta6Br12 cluster soaked crystal data. How can I define the cluster? How much of F'' and F' of this cluster at the wavelength of 1.254A?

Thank you.

Lisa _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk