We've had good luck (sometimes) searching for nucleic acids with multiple small pieces - say ask it to find several 5bp chunks of DNA rather than one 20bp duplex. I think Bill Scott will agree? I have a hunch that searching for the protein 1st, at least at "modest" resolutions, may confuse the software because the DNA is denser. Of course, every case has its own idiosyncracies. Phoebe
---- Original message ---- >Date: Tue, 10 Nov 2009 14:19:43 -0500 >From: Christian Biertuempfel <biertumpf...@niddk.nih.gov> >Subject: Re: [ccp4bb] molecular replacement in phaser >To: CCP4BB@JISCMAIL.AC.UK > >Hi Lisa, >There are many things you can try and the phaser manual gives a lot of >useful information what to do in difficult cases. From my experience, it >is quite difficult to find solutions for MR with nucleic acids. I >recommend to search only for protein. As a side effect you can use this >approach as an "unbiased" quality check. If your solution is correct you >expect to see additional density coming up for RNA (assumed that the RNA >is ordered). >Try different protein models containing either C-term or N- term or both. >Homology modeling can help a lot to generate a good search model. Try >also to give higher values for rms differences (or lower sequence >identity) between search model and target. Do you allow too many clashes >as a packing criterion? > >Cheers, >christian > >p.s. Of course, check that you work in the right space group. > > >Lisa Wang wrote: >> Hi all, >> I got one data about 3.0 A, belong to C2 space group. There are two >> protein molecules and one 18-nt dsRNA per ASU. The structure of last >> 100aa (C-terminal) has been reported, and 400 aa at N- terminalhe has >> homology structure with sequence identiy 30%. I try to solve it by MR >> with phaser. >> I did rotation and tranlation with 18-nt ideal dsRNA first, then search >> with C-terminal model. I got about 20 sol after seaching dsRNA with TFZ >> 8-10.0. I use all of them to serch the first c-terminal, and second >> C-terminal. Ding this process, LLG keep on increasing, and TFZ is >> higher than 10. But all have serious clash. It looks like all the sol >> are wrong. >> >> Please give me a hand. Phoebe A. Rice Assoc. Prof., Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 RNA is really nifty DNA is over fifty We have put them both in one book Please do take a really good look http://www.rsc.org/shop/books/2008/9780854042722.asp
