Hi, There's one big difference between macromolecular and small molecule refinement: except at ultra-high resolution the bond lengths in the former are almost always strongly restrained, whereas those in the latter are almost without exception completely unrestrained (except possibly bond lengths to H atoms in XRD). In other words, MX accurately determines the orthogonal atomic co-ordinates, whereas XRD accurately determines their fractional co-ordinates (it's no accident that the different programs output co-ordinates in those formats).
This means that since the cell dimensions are then used to convert fractional to orthogonal in XRD, the final bond lengths will be much more sensitive to errors in the cell dimensions, so having accurate cell dimensions is more critical if you want accurate bond lengths (e.g. for use as restraints in MX!). Obviously there's also a limit to the errors in the cell dimensions that can be tolerated in MX: large errors will lead to errors in calculated d* values and hence the scattering factors, which is likely to have a significant effect, and there may be issues with VdW repulsions if the cell is too small (though it's relatively easy for the structure to accommodate that). As Philip pointed out, the bond lengths will be totally insensitive to errors in the uncertainties of the cell dimensions, whether artificially introduced or poorly estimated from the data. I don't know of any MX refinement program (other than Shel-X) that takes the uncertainties in the cell dimensions into account, even assuming that you have accurate values for them. Also you should be careful not to confuse uncertainty (imprecision) with error (inaccuracy). The 'standard uncertainty' (s.u.) is the experimental estimate of the 'standard deviation' (in the error) ( https://physics.nist.gov/cgi-bin/cuu/Info/Constants/definitions.html), and the old term 'estimated standard deviation' (e.s.d.) was deprecated in 1993 (http://scripts.iucr.org/cgi-bin/paper?S0108767395002340). You can have an error in an uncertainty (which is what you were introducing in your test), but you can't have an uncertainty in an error, since errors are by their nature unknown anyway! It goes without saying that it's not a good idea to use bond lengths from a restrained refinement as restraints in other refinements! Cheers -- Ian On Wed, 15 Jul 2020 at 17:56, Jeffrey B Bonanno < jeffrey.bona...@einsteinmed.org> wrote: > Hi Phil, > > > > Being young and impressionable, I only changed ZERR, and you are quiet > right the result is the rigorous and expected error propagation of shelxl. > Of course the more fun experiment would be in systematically changing > various values in UNIT to watch the molecule distort. > > > > Hope all is well, > > jbb > > > > Jeffrey B. Bonanno, Ph.D. > > Department of Biochemistry > > Albert Einstein College of Medicine > > 1300 Morris Park Avenue > > Bronx, NY 10461 > > off. 718-430-2452 fax. 718-430-8565 > > email jeffrey.bona...@einsteinmed.org > > > > *From:* Jeffrey, Philip D. <pjeff...@princeton.edu> > *Sent:* Wednesday, July 15, 2020 12:47 PM > *To:* CCP4BB@JISCMAIL.AC.UK; Jeffrey B Bonanno < > jeffrey.bona...@einsteinmed.org> > *Subject:* Re: [ccp4bb] Quote source inquiry > > > > *CAUTION: This email comes from an external source; the attachments and/or > links may compromise our secure environment. Do not open or click on > suspicious emails. Please click on the “Phish Alert” button on the top > right of the Outlook dashboard to report any suspicious emails.* > > :: took a working dataset and increased (only) the error on unit cell > dimensions in the instruction file for the final round of full matrix :: > least squares refinement in shelxl. Sure enough, the errors on the bonds > and angles shot up. I was more careful > > > > Question: did you change the unit cell dimensions (UNIT) or the reported > standard error in the unit cell dimensions (ZERR) ? If just the latter > don't you think that the error propagation is just a factor of SHELXL > converting from fractional to orthogonal coordinates to give you bond > lengths and bond angles (i.e. the bonds and angles would be numerically the > same, but the estimated error associated with them would be higher). Did > the e.s.d.'s of the actual coordinates in fractional space change ? > > > > Phil Jeffrey > > Princeton > ------------------------------ > > *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Jeffrey > B Bonanno <jeffrey.bona...@einsteinmed.org> > *Sent:* Wednesday, July 15, 2020 12:36 PM > *To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > *Subject:* Re: [ccp4bb] Quote source inquiry > > > > Hi Gerard and Bernhard, > > As a postdoc in an unnamed small molecule lab, I was instructed by my lab > head to get better unit cell estimates prior to data collection owing to > error propagation from the uncertainty on cell dimensions through to the > esd on atomic bond lengths and angles when refining in shelxl. To verify > this (what, you believed everything your postdoc advisor told you?), I took > a working dataset and increased (only) the error on unit cell dimensions in > the instruction file for the final round of full matrix least squares > refinement in shelxl. Sure enough, the errors on the bonds and angles shot > up. I was more careful in determining the unit cell thereafter. That is, > until, I became a macromolecular crystallographer... > > After an inciteful (sp? lol) discussion with Wladek about cell dimensions, > I was directed to read this paper: > > Acta Crystallogr D Biol Crystallogr. 2015 Nov 1; 71(Pt 11): 2217–2226. > > Have a look, it is interesting. > > Having never followed up on these studies to see what happened to bonds > and angles in proteins and their ligands when varying cell dimensions, I > can't say with any confidence. However, I would guess that the quality of > the refined ligand coordinates could only be as good as some combination of > factors including but not limited to 1) the data (resolution, B factor, > etc), 2) the actual occupancy of the ligand, and 3) the restraints employed. > > jbb > > Jeffrey B. Bonanno, Ph.D. > Department of Biochemistry > Albert Einstein College of Medicine > 1300 Morris Park Avenue > Bronx, NY 10461 > off. 718-430-2452 fax. 718-430-8565 > email jeffrey.bona...@einsteinmed.org > > > -----Original Message----- > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Gerard DVD > Kleywegt > Sent: Wednesday, July 15, 2020 11:49 AM > To: 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 > > > > <https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww. > <https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.%0b>> > hofkristallamt.org%2F&data=02%7C01%7Cjeffrey.bonanno%40einsteinmed > > .org%7Cf0b1878c0df040bb2e5308d828d6b0ed%7C9c01f0fd65e040c089a82dfd51e6 > > 2025%7C0%7C0%7C637304250594203532&sdata=9FFCpYd9D%2BrHR48DtL%2BglM > > W2dbZ%2FmSTw0fF88XRwR7o%3D&reserved=0> > > https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.h > > ofkristallamt.org%2F&data=02%7C01%7Cjeffrey.bonanno%40einsteinmed. > > org%7Cf0b1878c0df040bb2e5308d828d6b0ed%7C9c01f0fd65e040c089a82dfd51e62 > > 025%7C0%7C0%7C637304250594203532&sdata=9FFCpYd9D%2BrHR48DtL%2BglMW > > 2dbZ%2FmSTw0fF88XRwR7o%3D&reserved=0 > > > > <mailto:b...@hofkristallamt.org <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://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww. > > jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&d > > ata=02%7C01%7Cjeffrey.bonanno%40einsteinmed.org%7Cf0b1878c0df040bb2e53 > > 08d828d6b0ed%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637304250594 > > 203532&sdata=MdVq312BDC5B6EjIyAEaGjDXt%2B9SsSjIaw%2FH9Nxfemg%3D&am > > p;reserved=0 > > > > This message was issued to members of > > https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.j > > iscmail.ac.uk%2FCCP4BB&data=02%7C01%7Cjeffrey.bonanno%40einsteinme > > d.org%7Cf0b1878c0df040bb2e5308d828d6b0ed%7C9c01f0fd65e040c089a82dfd51e > > 62025%7C0%7C0%7C637304250594203532&sdata=25UsGO%2FeC2aTI9f0puoG5nh > > SUKhyCoMeVRKgQdncy7k%3D&reserved=0, a mailing list hosted by > > https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.j > > iscmail.ac.uk%2F&data=02%7C01%7Cjeffrey.bonanno%40einsteinmed.org% > > 7Cf0b1878c0df040bb2e5308d828d6b0ed%7C9c01f0fd65e040c089a82dfd51e62025% > > 7C0%7C0%7C637304250594203532&sdata=ATQYFzhj6lreD1vETky3HaN2N8opg5x > > 3szRPRRZ6fwc%3D&reserved=0, terms & conditions are available at > > https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww. > > jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=02%7C01%7Cjeffrey.bonan > > no%40einsteinmed.org%7Cf0b1878c0df040bb2e5308d828d6b0ed%7C9c01f0fd65e0 > > 40c089a82dfd51e62025%7C0%7C0%7C637304250594203532&sdata=NmdJIawDMh > > tarwNE8w4ssEYxAGzp0drlc3mNXwTdbgo%3D&reserved=0 > > > > > Best wishes, > > --Gerard > > ****************************************************************** > Gerard J. 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