Dear JiYG, With an unknown number of 1000 aa monomers, you definitively have a challenging project! In that case, you will have to do some homework before running phaser:
1) The Matthews program should give you an indication how many monomers to expect. 2) P2 is a very low symmetry space group, so it might indeed be a good idea to process in P1 and run MR in P1. 3) With a lot of crashes (clashes?) you may have to truncate exposed loops from your model. If a number of homologous structures are available in the pdb, you could superimpose them, truncate the loops that are different and use the ensemble as a search model. 4) How good is your search model, e.g. what is the %identity or homology? If the model is quite remote, MR might be difficult. In the CCP4, there is now a whole collection of automatic MR packages: Molrep, MrBUMP, Balbes, AMPLE, MoRDA, SIMBAD etc. you could try these as well. It will mainly take CPU time, not your time. Good luck! Herman Von: 苏纪勇 [mailto:sujy...@nenu.edu.cn] Gesendet: Dienstag, 8. Mai 2018 17:03 An: Schreuder, Herman /DE Cc: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: AW: [ccp4bb] tNCS problem Dear Herman, I tried phaser. It worked. But there are a lot of crashes in the structure. Meanwhile, R factors could not be lowered. I tried to use P1 to process the data, but I do not know how many monomers in the asymetric unit. Bests, JiYG On 05/08/2018 22:50, herman.schreu...@sanofi.com<mailto:herman.schreu...@sanofi.com> wrote: Dear JiYG, Unless the tNCS has caused processing problems, Phaser should automatically deal with tNCS and I would recommend to just give it a try. If it fails, you could try more sophisticated approaches. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von ??? Gesendet: Dienstag, 8. Mai 2018 16:41 An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Betreff: [EXTERNAL] [ccp4bb] tNCS problem Dear all, Recently, I collected a data set of a crystal of a big protein, which contains 1000 amino acids. I processed the data to P2. But the data set has tNCS problem. I want to do molecular replacement. Is there anyone know how to deal with this problem? Thanks, JiYG
