Hi Lisa, I would start with learning AMoRe. It is relatively simple, runs fast and uses little memory, so you can experiment easily with lots of parameters. It is also relatively easy to modify the parameters, radii etc. and get a feel for which ones to use. If after a few days or weeks you understand AMoRe, you will have a good basic understanding of the practical aspects of molecular replacement. Also, most molecular replacement problems can be solved with it.
Molrep is also relatively fast, but a bit black-box compared to Amore. You can modify the search model to be more like the sequence of your protein by incorporating Chainsaw. This could lead to success in some cases where Amore might fail. For some difficult molecular replacement problems, the other programs will provide some benefits. Balbes basically tries to improve success by changing the search model, by trying lots of different ones automatically using the pdb as a source. I think it may also automatically incorporate Chainsaw? Phaser is very sophisticated, and probably therefore takes more time to run. It is incorporated both in CCP4 and Phenix and easy to set up and run from either GUI. Because the longer runtime, it is not so easy to experimentally test different search parameters, so to use these optimally it is better have a good understanding of molecular replacement. It does appear to solve some molecular replacement problems where other programs might fail. This is what I tell my students and is just my opinion and other, more expert crystallographers, might disagree on some of the points. (Of course, my students anyway just ignore me and always go for the GUI that looks hottest). Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 22 Apr 2013, at 09:05, LISA wrote: > Hi all, > There are so many software for MR, such as phaser, balbe,molrep, and amore. > What is difference between them? Which one is powerful? > Please give some comments for these software?Thank you. > > Sincerely, > lisa
