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Bill I already had reasoned exactly as you, but I never tried it: should be possible to run molecular replacement only with anomalous data and only with bromine positions from a reasonable model (because, as you said, one may expect Aform helices). But PC refinement should probably be used. And I guess, some luck is needed... Apart that, don't forget bromine cleavage under X-rays ... Ennifar et al. ActaCryst D58 (2002) 1262 Schiltz et al. ActaCryst D60 (2004) 1024 I suggest you to ask Clemens Vonrhein the new version of Sharp that is able to handle varying bromine occupancies during data collection. (as described in Schiltz et al) Good luck Philippe Dumas IBMC-CNRS, UPR9002 15, rue René Descartes 67084 Strasbourg cedex tel: +33 (0)3 88 41 70 02 [EMAIL PROTECTED] -----Message d'origine----- De : [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] la part de William Scott Envoyé : mercredi 30 aout 2006 20:16 A : [email protected] Objet : [ccp4bb]: a MAD molecular replacement question *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** Hi folks: I have a question regarding a Br mad data set on RNA. We have a crystal of an RNA in the lab in which the molecule has been transcribed and incorporates 11 Br-U residues at known positions in the sequence, and we have a MAD data set on this to about 3 A resolution (as well as a native data set). mmtbx.xtriage reports that we may have up to 3 molecules in the asymmetric unit (of P21), meaning 11, 22 and 33 Br sites are possible: ---------------------------------------------------------------- | Copies | Solvent content | Matthews Coef. | P(solvent cont.) | |--------|-----------------|----------------|------------------| | 1 | 0.828 | 7.146 | 0.012 | | 2 | 0.656 | 3.573 | 0.238 | | 3 | 0.484 | 2.382 | 0.652 | | 4 | 0.312 | 1.786 | 0.091 | | 5 | 0.140 | 1.429 | 0.007 | ---------------------------------------------------------------- | Best guess : 3 copies in the asu | ---------------------------------------------------------------- I've been using ShelxD to find Br sites, and the maps, though quite promising, still need significant improvement. I also haven't convinced myself that there is a clear NCS 2-fold or 3-fold, and so have been trying with 1,2, and 3 molecules. Since there are regions of this molecule that (presumably) have canonical A-form RNA helices, and these have Br-U in them at known positions, I'd like to make use of the distance constraints these put on the Br sites, as well as the Br absorption in the mad peak data. Is it possible to do molecular replacement using the Br anomalous signal and model helices to help pin down the locations of the Br atoms? Thanks in advance. Bill Scott -- No virus found in this incoming message. Checked by AVG Free Edition. Version: 7.1.405 / Virus Database: 268.11.7/432 - Release Date: 29/08/2006 -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.405 / Virus Database: 268.11.7/432 - Release Date: 29/08/2006
