30% is getting difficult - it may or may not work. But it is worth trying. Search model preparation programs such as Chainsaw rely on an accurate sequence alignment (between model and target), and this also gets difficult at 30%. You should try something more sophisticated than simple pairwise alignment: profile-profile alignment and/or something that uses the structural information of the search model template (FFAS, 3DCoffee, etc, etc - there seem to be lots).
Lots of useful tips in the proceedings of the 2007 Study Weekend (Acta Cryst D, published in Jan 2008 - I know this confuses some people ;) Cheers Martyn On Mon, 2009-06-22 at 10:15 +0800, 孙建 wrote: > Dear all: > Recently,I have a problem about molecular replacement with > identity 30% model. There are two moleculars in AU.Through > self-rotation analyze,there are a two-fold axis in AU along X axis or > Z axis.Then I rotate and translate the model with CNS MR module. > several models have been searched according self-rotation criterion.I > build the model using Phenix and Arp/wArp,but there are no good > results.The best result is R/Rfree 0.47/0.48.Also,I do MR with Phaser > and Molrep.The Phaser indicate Z-scores 6.5 and no good > results,neither do the Molrep.I am very confused about several > questions: > 1.Just 30% identity model can be used for MR model?What at > least identity should be acquired for MR? > 2.Are there good program editing the model except Chainsaw? > 3.How can I make sure my rotated and translated MR model is > right and can be used for next model building and refinement? > > -- *********************************************************************** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455 E-mail: martyn.w...@stfc.ac.uk * * Fax: +44 1925 603825 Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***********************************************************************
