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On Tue, 22 Aug 2006, Bernhard Rupp wrote: > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > > at the resolution you're working at the RMSD on bond > > lengths should be ca. 0.012, not 0.02 A. > > Interesting statement. I agree that for > very well determined small molecule structures, the > overall bond length variation is about 0.014 A or so. > > That fits quite well with what you say. It just means > that the structure should be restrained to reflect > reality. > > But: What does coordinate rmsd exactly have to do with > resolution? If the 3.5 A structure has 0.012 A > rmsd, does that mean that a 1.2 A structure > should have 0.005? I have a feeling that would > be a serious case of over-restraining. > > Should not all structures reflect the same > 'real world' rmsd (plus minus some minor individuality) > if the restraint weights are properly selected? > > Maybe the small molecule/shelxl fellows may chime in here: > What is the expected rmsd for a high res protein > structure vs. a low res? I had a feeling that > super low rmsd is partly abused as a sign of crystallographic > prowess, like building fantasy stuff into nonexistent density > just to have no missing residues &c &c &c... > > Thx, br Hi Bernhard, What I wrote means that unless you have superhigh resolution (in which case you can simply forget about library restraining --- you can even count the number of electrons for one atom to assign its type) the model should reflect reality. You state that reality is RMSD = 0.014, I thought it was 0.012 A. Small mistake from my part. Anyway the message was simply to state that targetting an RMSD of 0.02 meant that the geometry was not restrained tightly enough to fit what one expects at a resolution where unrestrained refinement cannot be done (who would attempt unrestrained refinement at 3.4 A refinement?). Fred. -- s-mail: F.M.D. Vellieux (B.Sc., Ph.D.) Institut de Biologie Structurale J.-P. Ebel CEA CNRS UJF 41 rue Jules Horowitz 38027 Grenoble Cedex 01 France Tel: (+33) (0) 438789605 Fax: (+33) (0) 438785494 e-mail: [EMAIL PROTECTED]
