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Re: [ccp4bb] bond lengths, angles, ideality and refinements |
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CCP4bb navigationCCP4bb <-- 2008 <-- January 2008 <-- 09 January 2008Subject: Re: bond lengths, angles, ideality and refinements From: "Nave, C (Colin)" colin {- dot -} nave {- at -} DIAMOND {- dot -} AC {- dot -} UK Date: 2008-01-09 The latest Acta D shows the "social consensus" is sometimes lacking even (or especially) among very experienced and able crystallographers. Experimental determination of optimal root-mean-square deviations of macromolecular bond lengths and angles from their restrained ideal values Ian J. Tickle pages 1274-1281 Numerology versus reality: a voice in a recent dispute Mariusz Jaskolski , Miroslaw Gilski , Zbigniew Dauter and Alexander Wlodawer pages 1282-1283 Interesting debate Colin -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of William Scott Sent: 09 January 2008 17:32 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] bond lengths, angles, ideality and refinements Sorry, that should have read "because the value is established by social consensus, it is thus NOT guaranteed to be perfectly accurate, ..." In other words, one can imagine some source of systematic error in establishing an ideal bond length. For example, the crystal packing environment of small molecules might tend to distort a bond by a couple hundredths of an Ångstrom. William Scott wrote: > Dear Yang Li: > > > Happy New Year to you, too, (ahead of Feb. 7th). > > You certainly owe us no apology; the reverse may not be true. > > Your question is an important one, as is what you have written below. > > I'm not certain I have a completely satisfactory answer. > > The reason is that ideal bond lengths may or may not be "true" in the > sense that the value is established by social consensus, and is thus > guaranteed to be perfectly accurate, even though it may be quite precise. > > Because of this, and because of natural deviations from ideality > (which really only become trustworthy observations at extremely high > resolution), a certain amount of "wiggle room" is typically allowed in terms of rmsd. > > The more conservative the refinement, the smaller the rmsd from > ideality will be. > > Some people believe 0.02 Å deviation from ideality is reasonable, > based on the accuracy of the dictionary values of bond lengths and > angles; others consider that to be "too sloppy" and a way to > artificially deflate Rfactors. > > I seem to have detected a tendency in the literature to aim for about > 0.01 Å deviation. The new refinement program phenix.refine, which is > supposed to optimize weighting between X-ray terms and stereochemical > constraints automatically, seems to settle in at quite conservative > values, such as > 0.005 Å, whereas with refmac, I can't seem to get the geometry any > more ideal than 0.005 Å even if I try to idealize a structure in the > absence of X-ray data. > > So, like you, I am a bit confused, and wouldn't mind hearing more from > the experts. > > All the best, > > Bill > > > > > > > yang li wrote: >> Dear All, >> I am very sorry to involve you into such insignificance >> discussion, I have reached agreement with Prof Gerard, please stop >> talking about things beyond science, thanks! >> I read a book today, which said "A refined model should exhibit >> rms deviations of no more than 0.02A for bond length and 4 for bond >> angels", I just wonder about the standard of the bond length and the >> bond angel. I think most of you have read similar words! >> But maybe I >> didnot express clearly and made some phrasal mistakes. >> At last, happy new year to you all--though very late! >> >> >> Sincerely! >> Yang Li >> > This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom CCP4bb navigationCCP4bb <-- 2008 <-- January 2008 <-- 09 January 2008 |
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