Hello, being a pedant, I guess you mean 'cell':
http://xray.chem.ualberta.ca/xray/shelxl/cell.htm rather than 'unit': http://xray.chem.ualberta.ca/xray/shelxl/UNIT.htm ;-? Best wishes, Jon Cooper -------- Original Message -------- On 15 Jul 2020, 17:55, Jeffrey B Bonanno 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 >> >> +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. Kleywegt > > [https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fxray.bmc.uu.se%2Fgerard&data=02%7C01%7Cjeffrey.bonanno%40einsteinmed.org%7Cf0b1878c0df040bb2e5308d828d6b0ed%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637304250594213524&sdata=2Ez3xflhrW7Gq4HZvxs5pI3BjBkdmRKPRLGqwVKXkRc%3D&reserved=0](https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fxray.bmc.uu.se%2Fgerard&data=02%7C01%7Cjeffrey.bonanno%40EINSTEINMED.ORG%7C75393f4ae01f4cfe500c08d828dec65a%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637304284576642982&sdata=JcKAV3x%2FOgqeUatm0Ziur9qUf2E3rZEf3iLJ6Lbo9pA%3D&reserved=0) > 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://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=02%7C01%7Cjeffrey.bonanno%40einsteinmed.org%7Cf0b1878c0df040bb2e5308d828d6b0ed%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637304250594213524&sdata=xCu9oAqFZa0n0RXM8lRxInioCMd1gaLPz5hWeAb6KB4%3D&reserved=0](https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=02%7C01%7Cjeffrey.bonanno%40EINSTEINMED.ORG%7C75393f4ae01f4cfe500c08d828dec65a%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637304284576642982&sdata=JhU0T0skyG7jqA8WiXYWoxQDtDya%2BcjSveASvgcv%2BfM%3D&reserved=0) > > This message was issued to members of > [https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=02%7C01%7Cjeffrey.bonanno%40einsteinmed.org%7Cf0b1878c0df040bb2e5308d828d6b0ed%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637304250594213524&sdata=wJQoDJF6Zasi4Q8saiHXW3%2FFy6OCz3mjbr5%2Bkcz%2BjA0%3D&reserved=0](https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=02%7C01%7Cjeffrey.bonanno%40EINSTEINMED.ORG%7C75393f4ae01f4cfe500c08d828dec65a%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637304284576652976&sdata=2VXjeWNn%2BbnDwSxg8tnoHws88lEei0Jp5h8z7R05NvQ%3D&reserved=0), > a mailing list hosted by > [https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=02%7C01%7Cjeffrey.bonanno%40einsteinmed.org%7Cf0b1878c0df040bb2e5308d828d6b0ed%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637304250594213524&sdata=SudzcHtpEhfM8Eqg%2BIgy2eonD0lQ8S1jNDx4OOt5CB8%3D&reserved=0](https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=02%7C01%7Cjeffrey.bonanno%40EINSTEINMED.ORG%7C75393f4ae01f4cfe500c08d828dec65a%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637304284576652976&sdata=R2vbxgobWgzWxG9W%2FUcFwY8Pfu%2BKsgw8DK77zTb6qDs%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.bonanno%40einsteinmed.org%7Cf0b1878c0df040bb2e5308d828d6b0ed%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637304250594213524&sdata=s4u0npGJy5i%2BT5SiHO8xDu%2BrdKwkfUp6UmfphtS6HZE%3D&reserved=0](https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=02%7C01%7Cjeffrey.bonanno%40EINSTEINMED.ORG%7C75393f4ae01f4cfe500c08d828dec65a%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637304284576662971&sdata=duLUjngtcSkRMhQHAYT%2BLBzCnQSxZgIx%2Fr3GC7O%2FUbA%3D&reserved=0) > > ######################################################################## > > 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://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=02%7C01%7Cjeffrey.bonanno%40EINSTEINMED.ORG%7C75393f4ae01f4cfe500c08d828dec65a%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637304284576662971&sdata=EveB8ltqCxA6kxuxoQIPFyDRTBeebqwgzAGw74sGJ%2Bw%3D&reserved=0) > > This message was issued to members of > [www.jiscmail.ac.uk/CCP4BB](https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=02%7C01%7Cjeffrey.bonanno%40EINSTEINMED.ORG%7C75393f4ae01f4cfe500c08d828dec65a%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637304284576672963&sdata=ccw3VsG4YMxuHekjxeqhu8zXe0IdO6lOgtZ65RmJVdA%3D&reserved=0), > a mailing list hosted by > [www.jiscmail.ac.uk](https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=02%7C01%7Cjeffrey.bonanno%40EINSTEINMED.ORG%7C75393f4ae01f4cfe500c08d828dec65a%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637304284576672963&sdata=oZyVNNL41INOhcr%2Fsdg2syaEHF1Xw2SdPM9Gnbn%2FOA4%3D&reserved=0), > terms & conditions are available at > [https://www.jiscmail.ac.uk/policyandsecurity/](https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=02%7C01%7Cjeffrey.bonanno%40EINSTEINMED.ORG%7C75393f4ae01f4cfe500c08d828dec65a%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637304284576682955&sdata=BPJorHnIfzvDudcxzwK6bTwFX05Yv62Sglx8pi%2BmxOE%3D&reserved=0) > > --------------------------------------------------------------- > > To unsubscribe from the CCP4BB list, click the following link: > 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/
