Hi Robbie Yes I was (perhaps rashly!) assuming that the data are properly weighted relative to the restraints.
Thanks for pointing that out. Cheers -- Ian On Wed, 15 Jul 2020 at 20:23, Robbie Joosten <robbie_joos...@hotmail.com> wrote: > 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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