Dear Thierry, ----- Le 31 Juil 20, à 21:58, Fischmann, Thierry <000022f7fda0a875-dmarc-requ...@jiscmail.ac.uk> a écrit :
> Jim wrote: > “ technically, not in Phenix either. The real-space refinement in Phenix > simply > picks peaks in the density and then pulls nearby atoms toward them. . Like a > black hole gobbling up nearby planets (snip)” > Do you have a reference to support this assertion The methodology of the "dirty but very fast" real space refinement in Phenix is described in detail in the article : Afonine, P.V.et al. (2018) "Real-space refinement in PHENIX for cryo-EM and crystallography". Acta Cryst ., D 74 , 531-544. The articel contains also arguments for such kind of procedure, its advantages (the principal goal and advantage is a very high speed) and obvious limitations (one of them mentioned by James). > Hopefully someone from the Phenix team will give some clarifications. But the > statement above indicates that Phenix is capable of performing real space > refinement by some other means than the “black hole approach” Sorry, here I cannot comment. Best regards, Sacha Urzhumtsev ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
