Close enough verbatim and dead on in spirit. Many thanks, BR -----Original Message----- From: Gerard DVD Kleywegt <ger...@xray.bmc.uu.se> Sent: Wednesday, July 15, 2020 08:49 To: b...@hofkristallamt.org Cc: CCP4 Bulletin Board <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Quote source inquiry
Well, I've had this in my CSHL X-ray Course talk for many years. In the attached 2007 Acta D paper it says (p 95): "Macromolecular X-ray crystallography is a notoriously poor method for determining the structure of small molecules that are bound to macromolecules [...]" and then goes on to explain why this is the case. In the attached 2003 paper (pooling the wisdom of several of the usual suspects, including Eleanor) it says something similar (p 1057): "Coordinates of molecules that have been determined in complex with macromolecules previously can of course also be retrieved from the PDB (Bernstein et al., 1977; Berman et al., 2000), HIC-Up (Kleywegt and Jones, 1998), or CHEMPDB (Boutselakis et al., 2003). However, one should keep in mind that these coordinates are the result of refinement against comparatively low-resolu- tion data where the small molecule constituted only a minute fraction of the total scattering matter. This makes these coordinates inherently much less accurate than those obtained from the CSD. In addition, the coordi- nates may contain errors due to the use of incorrect restraints. Hence, such coordinate sets should only be used as a last resort, and only after verification that they are reliable. The latter can be facilitated by inspection of the electron density for the compound in question, for instance at the Uppsala Electron-Density Server (http:// fsrv1.bmc.uu.se/eds) (G.J.K. et al., submitted)." Happy to be confused with George though! --Gerard (no, the other one) On Tue, 14 Jul 2020, Bernhard Rupp wrote: > Hi Fellows, > > > > afaicrimps (as far as I can recall in my progressing senility) > someone once wrote/stated/cursed somewhere that "Macromolecular > refinement is not a small molecule structure determination method". > > > > Any citable source - George Sheldrick might be a suspect. > > > > Thanks & best regards, BR > > > > ------------------------------------------------------ > > Bernhard Rupp > > <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/ > > <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org > > +1 925 209 7429 > > +43 676 571 0536 > > ------------------------------------------------------ > > Many plausible ideas vanish > > at the presence of thought > > ------------------------------------------------------ > > > > > ###################################################################### > ## > > 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/ > Best wishes, --Gerard ****************************************************************** Gerard J. Kleywegt http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se ****************************************************************** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ****************************************************************** Little known gastromathematical curiosity: let "z" be the radius and "a" the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! ****************************************************************** ######################################################################## 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/
