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 <ianj...@gmail.com> 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 > >
