Dear Tim,
I know that it cause rescaling and you don't have to input the number
manually most of the time recently. I just wanted to point out that it
can obviously happend. The question reminded me Andrea's lecture.
Jan
On 07/02/2015 10:34 AM, Tim Gruene wrote:
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Dear Jan,
when you input the wrong wavelength during data processing, you
rescale the Ewald sphere construction, i.e. it will result in a
different unit cell and crystal to detector distance.
I am not sure what you mean by 'which no program from
integration to structure solution did not recognised'. How should the
downstream software detect the human mistake?
The wavelength you enter should of course be double checked.
Nowadays this seldomly occurs because the experimental settings are
usually transferred automatically and reliably between the beamline
software and the processing tools.
Cheers,
Tim
On 07/02/2015 09:27 AM, Jan Stransky 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 <ianj...@gmail.com
<mailto: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
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
phone: +49 (0)551 39 22149
GPG Key ID = A46BEE1A
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1
iD8DBQFVlPeFUxlJ7aRr7hoRAuQXAJ4gYxRxL/BELbrDGpAxUXbUErBPgwCghcsv
nEVcp0relCBO/HVt9poCnYE=
=V1FJ
-----END PGP SIGNATURE-----
--
Jan Stransky, PhD student
Institute of Biotechnology, CAS
Laboratory of structure and function of biomolecules
Nad Safinou II 366
Vestec
Czech Republic
Tel.: +420226201570
