Hi Jan Thanks for the suggestion. I checked & AFAICS the wavelength is correct. I think in any case the difference you are talking about would be far too small to explain the effect I'm seeing (the error in the wavelength is ~ 0.01% whereas I'm seeing deviations from the ideal vdW contact of up to 15%!).
My conclusion is that this is not due to any kind of error, it is a real effect. CH...O bonds are well-documented (thanks to Patrick Loll and Scott Horowitz for useful references), even though it appears that MP (and PDB validation) takes absolutely no account of them! Cheers -- Ian On 2 July 2015 at 08:27, Jan Stransky <[email protected]> wrote: > About the unit cell shrinkage: > > I have heard a lecture (I believe it was Andrea Thorn form G. Sheldrick > group on one of CCP4 meetings), where she mentioned a mistake in X-ray > wavelenght input (swaped 3rd and 4th digit), which no program from > integration to structure solution did not recognised. It appeared in > structure refinement in wrong bond distances. > > Worth of checking. > > Jan > > > On 07/01/2015 10:58 AM, Ian Tickle wrote: > > > Paul, as an aside to this, would it be possible to have it so that if the > relevant boxes in the "Environment Distances" menu are checked then H-bonds > and.or bumps are automatically re-calculated on re-centering? Currently > it's necessary to check off & on one of the boxes every time the view is > re-centered. If I forget to do that it's very easy to miss bumps (and I > don't have a great deal of faith in MP's concept of what constitutes a > bump)! > > Cheers > > -- Ian > > > On 30 June 2015 at 14:33, Ian Tickle <[email protected]> wrote: > >> >> Hello All >> >> I guess this is really a question about MolProbity (and possibly about >> autoBuster) but I assume that most Coot users will be using the MolProbity >> validation tools. >> >> I am in the process of depositing 4 structures of the same protein >> (different ligands) and I noticed that MP seems to be reporting an >> unusually large number of bumps in both the "small overlap" and "bad >> overlap" classes. In each case the resolution is 2 Ang., the structures >> have been refined by autoBuster and the density seems to be unequivocal, >> see e.g.: >> >> >> https://drive.google.com/file/d/0B4H4H-DyO60-SEQwS1k5S3RIVG8/view?usp=sharing >> >> A lot of the bumps are main-chain CHalpha to main-chain carbonyl O >> H-bonds, but there are also some CH...O side-chain H-bonds, again with >> clear density. The C...O distances are in the range 3.0 to 3.2 Ang., so >> too short for a vdW contact. The H...O distances are ~ 2.2 Ang. which is >> definitely shorter than the sum of the vdW radii ( H: 1.2 + O: 1.5 = 2.7). >> >> I found this survey of CH...O H-bonds but it's restricted to CH...O >> bonds at the end of helices and I see them mostly in sheets. >> >> http://www.mrc-lmb.cam.ac.uk/genomes/madanm/pdfs/chapter1.pdf >> >> This reports 11 examples (i.e. H-bonds, not structures) in the 3.0-3.2 >> range for the whole of the PDB (admittedly as it was in 2001 when the >> article appears to have been written). I have about the same number in one >> structure! >> >> One possibility I considered was that the unit cells had all somehow >> 'shrunk'. This can be tested with WhatCheck: however it only reports a >> very small shrinkage which translates to an error of ~ 0.02 Ang. in a 3 >> Ang. distance, which is nowhere near enough to explain a discrepancy of 0.5 >> Ang. >> >> So I guess my question is has anyone else noticed this in their MP >> dot-plots; also does anyone know what criteria does MP uses for testing >> bumps and specifically what value is it using for CH...O H-bonds? And of >> course I'd like to know whether this will affect my percentile ranking in >> the clashscore from the PDB validation! >> >> Cheers >> >> -- Ian >> >> > > -- > Jan Stransky, PhD student > Institute of Biotechnology, CAS > Laboratory of structure and function of biomolecules > Nad Safinou II 366 > Vestec > Czech Republic > > Tel.: +420226201570 > >
