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A follow up to this (for what it's worth) is that it's sometimes easier to solve a structure by MR from a homologous structure determined by experimental phases than it is to solve the initial structure by SeMet, MIR, etc. An example is the case of the structure determination of the second isoform of aspartate beta-semialdehyde dehydrogenase from Vibrio cholerae (vcASADH2). We had 2 Angstrom data and three molecules in the asu with <30% seq id to the previously determined structures and tried MR for quite a while without success. Then we made very slow progress with SeMet and other derivatives for much longer than I would like to admit. Once we decided to switch to the Methanococcus jannaschii ortholog (~40% seq. id to the vcASDAH2) we made much better progress. The structure of the MjASADH SeMet derivative was determined in a matter of weeks (Faehnle et al JMB '05) and the structure of the vcASADH2 ortholog was determined shortly thereafter (publication forthcoming). In the age of ultra-rapid MolBiol, evaluating other orthologs or constructs may be faster than sweating over a single construct. Jeff -----Original Message----- From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Bart Hazes Sent: Monday, January 22, 2007 8:08 PM To: [log in to unmask] Subject: Re: advice I'd like to add that the value of a molecular replacement solution tends to be inversely correlated with the effort needed to find the solution. In other words, the harder you have to work to find the MR solution the less informative the phase information you tend to get. When you have very high resolution and/or NCS you may still be able to solve the structure. However, in cases were the search model is only distantly related to the protein of interest and Phaser can't find the solution, the solution may not be worth finding and you're better of focussing on getting experimental phases. Bart Randy J. Read wrote: > On Jan 22 2007, Eaton Lattman wrote: > >> Will someone knowledgeable tell me what the present state of full 6 >> dimensional searches in molecular replacement? > > > Presumably you're referring to systematic 6D searches, not stochastic > ones like in EPMR or QoS. Do you mean "can it be done on current > hardware" or "is it worth doing"? If the former, then it's doable, > though slow. In Phaser, for instance, you can generate a complete list > of rotations (using the fast rotation function with keywords to > prevent clustering and to save all solutions), then feed that big list > of rotations to the fast translation search. In a typical problem that > would probably run on a single processor in significantly less time > than the average PhD, and could be made reasonably quick with a cluster. > > If the latter, our feeling is that it isn't worth it. We've tried the > full search option on a couple of monoclinic problems (where it's only > a 5D search), and nothing came up with the full list of orientations > that didn't come up with the first hundred or so orientations. > > We conclude that, even in the most recalcitrant cases, the rotation > search gives a better than random indication of whether an orientation > is correct, so it's not necessary to search through all possible > orientations. However, we do feel that it can be worthwhile to try a > reasonably large number of orientations in difficult cases. > > Best regards, > > Randy Read > > P.S. When we generate our list of orientations, we use "Lattman" > angles to get reasonably even sampling of rotations. > ---------------------------------------------------------------------- LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail or any action taken (or not taken) in reliance on it is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately.