As with Jurgen, I’ve never trimmed a residue. In my view the trimmed residues do not exist. If we were to build models consisting of only atoms defined by the experimental density, then I wonder what the original model of the DNA double helix would have looked like.
BTW, hey Jurgen, long time no talk. Cheers, Quyen ________________ Quyen Hoang, PhD Professor of Biochemistry and Molecular Biology Director of IUSM Center for Electron Microscopy (iCEM) Adjunct Professor of Neurology Primary Investigator of the Stark Neuroscience Research Institute Indiana University School of Medicine 635 Barnhill Drive, MS0013C Indianapolis, IN, 46202 (317)274-4371 https://qqhoang.pages.iu.edu > On Mar 10, 2023, at 12:09 PM, Jurgen Bosch <[email protected]> wrote: > > I’m sure James H. Is preparing a philosophical dissertation on the "State of > the atoms to B or not to B that is not only a refinement question” that he > will share momentarily with the board. > > Jürgen > >> On Mar 10, 2023, at 12:06 PM, DEBANU DAS <[email protected]> >> wrote: >> >> Yes, zero occupancy would reflect that. But not the coordinates in any >> proper way. >> Debanu >> >> On Fri, Mar 10, 2023 at 8:58 AM Jurgen Bosch <[email protected] >> <mailto:[email protected]>> wrote: >> Going back to RIP phasing methods :-) >> So Harry in your particular case occupancy of zero would actually reflect >> reality for those “combusted” atoms. >> >> Jürgen >> >> > On Mar 10, 2023, at 11:56 AM, Harry Powell >> > <[email protected] >> > <mailto:[email protected]>> wrote: >> > >> > Hi folks >> > >> > One other thing that I haven’t noticed anyone mentioning yet (sorry to >> > those who have mentioned it!!) is that you may not see your sidechain >> > atoms in density because they are not there at all, in spite of what you >> > may have had in the original protein, or even if the atoms were really >> > there in the crystal _before_ exposure to the beam. >> > >> > The coordinates are supposed to be what you actually find, not what you >> > hope is there. >> > >> > Just my two ha’porth >> > >> > Harry >> > >> > ######################################################################## >> > >> > To unsubscribe from the CCP4BB list, click the following link: >> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> > <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 >> > <http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by >> > www.jiscmail.ac.uk <http://www.jiscmail.ac.uk/>, terms & conditions are >> > available at https://www.jiscmail.ac.uk/policyandsecurity/ >> > <https://www.jiscmail.ac.uk/policyandsecurity/> >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <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 >> <http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by >> www.jiscmail.ac.uk <http://www.jiscmail.ac.uk/>, terms & conditions are >> available at https://www.jiscmail.ac.uk/policyandsecurity/ >> <https://www.jiscmail.ac.uk/policyandsecurity/> > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> ######################################################################## 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/
