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]
<mailto:[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
