Absolutely try Phaser! See Phaser documents for all the nifty combinations. Multiple molecules in MR model; break down molecule by domains etc etc. You can trim down side chains, make hybrid models and what not. All easy to get up and going through the GUI. Once the GUI drove me insane because of some 'hyphen' mark in the file name; sometimes I just prefer to set up scripts. Run to the documentation and examples, which are both pretty darned good. NO! I don't get paid by Randy.
However, given the low resolution and the ambiguities you describe, especially of the combination in the ASU and if the two subunits are closely related and of similar lengths, my hunch is that experimental phasing will become necessary at some point. Since you describe you have 2*AB in the ASU, first search for AB as search model. One way for internal check is to feed Phaser only Molecule A and ask to look for 4 molecules. Then, feed only Molecule B and look for 4 molecules. If all these results look the same, I'd be worried and I might think of SelMet-labeling one of the two molecules or something like that. Just some thoughts. Good luck and just download Phaser for starters. Raji ---------Included Message---------- >Date: 21-feb-2008 06:40:57 -0500 >From: "James Stroud" <[EMAIL PROTECTED]> >To: <CCP4BB@JISCMAIL.AC.UK> >Subject: [ccp4bb] Tough Low-Res MR > >Hello All, > >I have a tough ~3.5 Å (pushing it) MR problem where I have a solution >of sorts, but because I'm working with a heterodimer of two closely >related subunits (with two such heterodimers in the ASU) I have a 2**2 >possibilities for the arrangement of these subunits in the ASU. Each >subunit is composed of two more-or-less independent domains. Basically >I'm looking for the best possible software to disambiguate this >problem. I usually use CNS for these problems, but I think I may have >exhausted its capabilities. I've heard that there have been some >advances in MR in recent years, but I haven't kept up with all of the >software. Does anyone have suggestions for packages to try? > >James > >-- >James Stroud >UCLA-DOE Institute for Genomics and Proteomics >Box 951570 >Los Angeles, CA 90095 > >http://www.jamesstroud.com > > ---------End of Included Message----------
