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Dear Friends,
If possible, I would like to have some more explanationon this question.
Hi Alex,
as far as I understand, the WHATCHECK deformation matrix tries to figure
out any systematic deviations from ideal stereochemistry that could be the
result of systematically wrong cell dimensions. In practice, it
As systematically here you mean in all 3 cell parameters ? What if
(:-) ) you had one overestimated and one underestimated ? I think WHATCHECK
must somehow separate bond lenghts (eg) in each of the 3 components and from
this it takes its conclusions about each cell parameter. Am I right ?
usually detects systematic deviations between the built-in stereochemistry
library
What does built-in mean here ? Built-in in WHATCHECK ? Should it not be
the Engh-Huber parameters, like for instance the one in refmac5 ?
and the one that was used during refinement.
Yet one other question here is how should we expect a cell dimension to
change under cryocooling ...
When you modify the cell constants as suggested in the WHATCHECK output
and do a re-refinement, the next output will have similar complaints, and
so on. If you took care about proper data processing, the cell constants
should be usually well determined. In such a case, at least in my
experience, you can safely ignore the deformation matrix warnings in
WHATCHECK.
It is good to listen to Dirk's experience. Is it common sense that we
should, unless serious erros are around (eg, what about smeared spots in the
image, etc..), ignore WHATCHECK recommendation and go for the refined cell
in the image processing program ?
Jorge
Best regards,
Dirk.
Alex Gutteridge wrote:
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Hi,
I'm using WHATCHECK (http://swift.cmbi.ru.nl/gv/pdbreport/) to
scan some crystal structures for unit cell scaling problems. I'm doing
this because the analysis I want to do on these structures will be
sensitive to these kind of errors. At this point I should mention that
I'm not a crystallographer by trade, so forgive me if this is an
obvious/stupid question. WHATCHECK gives a 'deformation matrix' as part
of it's output in this section. Am I right in thinking that if the matrix
looks like this (from PDB code 2DHB):
0.987651 -0.000042 -0.000855
-0.000042 0.985582 -0.000365
-0.000855 -0.000365 0.987811
Then it is (essentially saying) the structure as given in the PDB file is
stretched about 1-2% (scale factor of 0.99-0.98) along each axis? And so
any measurement of length/distance in the structure will be 1-2% longer
than it should be? Also does anyone know of a program that can apply this
matrix to a PDB file to get the correctly scaled structure. I've found
one paper that implies they did this, but they don't really say how.
Thanks in advance!
Alex Gutteridge
EBI
Wellcome Trust Genome Campus
Hinxton
Cambs CB10 1SD
UK
Tel: 01223 492546
Email: [EMAIL PROTECTED]
--
****************************************
Dirk Kostrewa
Paul Scherrer Institut
Life Sciences, OFLC/110
CH-5232 Villigen PSI, Switzerland
Phone: +41-56-310-4722
Fax: +41-56-310-5288
E-mail: [EMAIL PROTECTED]
http://sb.web.psi.ch
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