Hi Ian, Errors in cell dimensions can have a large effect in MX with certain refinement doctrines. The school of "bond length rmsd must be $NUMBER" (which is still going strong unfortunately) will suffer from poor R-factors because the target cannot be satisfied without harming the fit to the data. At the same time if you have a a more relaxed approach to restraints than you might find systematic deviations in bond lengths. A test for that has been in WHAT_CHECK for decades and it actually works surprisingly well to detect cell dimension problems. That said, the problem is uncommon now.
Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Ian > Tickle > Sent: Wednesday, July 15, 2020 20:25 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Quote source inquiry > > > 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 > <mailto: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 > <mailto:jeffrey.bona...@einsteinmed.org> > > > > From: Jeffrey, Philip D. <pjeff...@princeton.edu> > Sent: Wednesday, July 15, 2020 12:47 PM > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> ; > Jeffrey B Bonanno <jeffrey.bona...@einsteinmed.org > <mailto: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 > <mailto:CCP4BB@JISCMAIL.AC.UK> > on behalf of Jeffrey B Bonanno > <jeffrey.bona...@einsteinmed.org > <mailto:jeffrey.bona...@einsteinmed.org> > > Sent: Wednesday, July 15, 2020 12:36 PM > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > <CCP4BB@JISCMAIL.AC.UK <mailto: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 > <mailto:jeffrey.bona...@einsteinmed.org> > > > -----Original Message----- > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK > <mailto:CCP4BB@JISCMAIL.AC.UK> > On Behalf Of Gerard DVD Kleywegt > Sent: Wednesday, July 15, 2020 11:49 AM > To: CCP4BB@JISCMAIL.AC.UK <mailto: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 > <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%2Fww > w. > <https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F > %2Fwww.%0b> > hofkristallamt.org <http://hofkristallamt.org> > %2F&data=02%7C01%7Cjeffrey.bonanno%40einsteinmed > > > .org%7Cf0b1878c0df040bb2e5308d828d6b0ed%7C9c01f0fd65e040c089a82d > fd51e6 > > > 2025%7C0%7C0%7C637304250594203532&sdata=9FFCpYd9D%2BrHR4 > 8DtL%2BglM > > W2dbZ%2FmSTw0fF88XRwR7o%3D&reserved=0> > > > https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww > .h > <https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fww > w.h> > > ofkristallamt.org <http://ofkristallamt.org> > %2F&data=02%7C01%7Cjeffrey.bonanno%40einsteinmed. > > > org%7Cf0b1878c0df040bb2e5308d828d6b0ed%7C9c01f0fd65e040c089a82df > d51e62 > > > 025%7C0%7C0%7C637304250594203532&sdata=9FFCpYd9D%2BrHR48 > DtL%2BglMW > > 2dbZ%2FmSTw0fF88XRwR7o%3D&reserved=0 > > > > <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org > <mailto: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%2Fww > w > <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fww > w> . > > jiscmail.ac.uk <http://jiscmail.ac.uk> %2Fcgi-bin%2FWA- > JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&d > > ata=02%7C01%7Cjeffrey.bonanno%40einsteinmed.org > <http://40einsteinmed.org> %7Cf0b1878c0df040bb2e53 > > > 08d828d6b0ed%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C6373 > 04250594 > > > 203532&sdata=MdVq312BDC5B6EjIyAEaGjDXt%2B9SsSjIaw%2FH9Nxfe > mg%3D&am > > p;reserved=0 > > > > This message was issued to members of > > > https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww > .j > <https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fww > w.j> > > iscmail.ac.uk <http://iscmail.ac.uk> > %2FCCP4BB&data=02%7C01%7Cjeffrey.bonanno%40einsteinme > > d.org <http://d.org> > %7Cf0b1878c0df040bb2e5308d828d6b0ed%7C9c01f0fd65e040c089a82dfd5 > 1e > > > 62025%7C0%7C0%7C637304250594203532&sdata=25UsGO%2FeC2aTI9 > f0puoG5nh > > SUKhyCoMeVRKgQdncy7k%3D&reserved=0, a mailing list > hosted by > > > https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww > .j > <https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fww > w.j> > > iscmail.ac.uk <http://iscmail.ac.uk> > %2F&data=02%7C01%7Cjeffrey.bonanno%40einsteinmed.org > <http://40einsteinmed.org> % > > > 7Cf0b1878c0df040bb2e5308d828d6b0ed%7C9c01f0fd65e040c089a82dfd51e > 62025% > > > 7C0%7C0%7C637304250594203532&sdata=ATQYFzhj6lreD1vETky3HaN > 2N8opg5x > > 3szRPRRZ6fwc%3D&reserved=0, terms & conditions are > available at > > > https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fww > w > <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fww > w> . > > jiscmail.ac.uk <http://jiscmail.ac.uk> > %2Fpolicyandsecurity%2F&data=02%7C01%7Cjeffrey.bonan > > no%40einsteinmed.org <http://40einsteinmed.org> > %7Cf0b1878c0df040bb2e5308d828d6b0ed%7C9c01f0fd65e0 > > > 40c089a82dfd51e62025%7C0%7C0%7C637304250594203532&sdata=N > mdJIawDMh > > tarwNE8w4ssEYxAGzp0drlc3mNXwTdbgo%3D&reserved=0 > > > > > Best wishes, > > --Gerard > > ******************************************************** > ********** > Gerard J. 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