Hi Randy, thanks for getting back to my email. Yes, I do think it would be very helpful to switch to using density instead of coordinates both for MR and MR-SAD. The interface between cryo-EM and X-ray is growing so fast that in many cases EM densities could be used for initial phasing by Fourier difference, or even ab initio, provided sufficient ncs is available. In our specific case we have at least two macromolecular complexes (1.1-2.2MDa) with >400SeMet, resolutions in the mid 3A with extreme unisomorphism and 10-15A EM densities. SAD/MAD phasing is unrealistic, MIR methods can't work when all crystals are inherently unisomorphic .... MR/MR-SAD could be an alternative. Thanks again! Gino Hi, As it happens, we've been working very hard over the last few months first to make all commands in Phaser available from Python (done) and second to make all options available from the new Phenix GUI (getting close). ("We" in this context mostly means Airlie at our end and Nat at the Berkeley end.) So it should become easy to switch to using density instead of coordinates for your models without switching to the command-line mode of running Phaser. We're also very interested in optimizing the way that we use density from EM, which is something we haven't spent enough time playing with yet. It's not yet possible to use density for a model in the MR-SAD mode--that's been on the wish list and shouldn't be too hard. Do you need that feature right now? I really like your other ideas, so we'll have to talk to Tom about adapting the AutoMR wizard so that it doesn't require a coordinate file. As you say, this will be a real growth area! All the best, Randy On 8 May 2009, at 15:39, Gino Cingolani wrote:

Hi Randy,

what about implementing the use of EM-models (e.g. structure factors from EM model) in Phenix to carry out MR and/or MR-SAD? There's a growing number of macromolecular complexes that have been imaged at medium/low res by EM, which could be of great help to phase at low res or located anomalous scatterers in phased maps. And the EM database keeps growing!

At this moment, it is certainly possible to use EM models in Phaser, but the Phenix pipeline could add much more to that. For instance, Phenix would allow for better phase extension of low res EM phases to higher res by ncs-averaging or multi-crystal averaging (in Resolve). Or Phenix could help combining low res EM phases with other phase sources such as SeMet sites, poorly occupied heavy atom sites, etc (MR-SAD). Or Phenix could rigid body refine (at low resolution) pseudo-atomic models obtained by filling in EM-models with dummy atoms. This would help defining averaging masks and so on. What do you think?

Thanks in advance,

Gino

*********************************************************** Gino Cingolani, Ph.D. Assistant Professor Dept. of Biochemistry and Molecular Biology SUNY Upstate Medical University 750 E. Adams Street, Syracuse, NY, 13210 Tel. (315) 464 8744 Fax. (315) 464 8750 Email: [email protected] *********************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) _______________________________________________ phenixbb mailing list [email protected] http://www.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 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb *********************************************************** Gino Cingolani, Ph.D. Assistant Professor Dept. of Biochemistry and Molecular Biology SUNY Upstate Medical University 750 E. Adams Street, Syracuse, NY, 13210 Tel. (315) 464 8744 Fax. (315) 464 8750 Email: [email protected] *********************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)