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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
usually detects systematic deviations between the built-in
stereochemistry library and the one that was used during refinement.
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.
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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