Quality Control and Validation - Supplementary Material
Supplementary material (hyperlinks and
example files) to:
Kleywegt, G.J. (2007 ?).
Quality control and validation.
In "Crystallographic Methods", S Doublie, Ed., Humana Press,
Totowa, NJ, in press
Hyperlinks mentioned in the chapter
- CCP4 home page
- Related to O:
- PDB home page
- Related to the Uppsala Software Factory (OOPS2, MAPMAN, MOLEMAN2):
- Validation tutorial
- Related to WHAT IF (and WHAT_CHECK):
Example files to try out the methods
If you download some of the folowing files, you will be able to
apply the methods described in the chapter. As a minimum, you
will need the model and the two maps. If you don't have access
to WHAT IF (or WHAT_CHECK), you can also download its results file.
To download files, use the "Save link as ..." feature of your
browser (usually activated by pointing at a link with your
cursor and then pressing some mouse button or buttons).
- The model (model.pdb) is one of
cellular retinoic-acid-binding protein type II (the final model,
1CBS, and its structure factors can be downloaded from the
This particular model has been made considerably worse by
introducing some errors in main-chain and side-chain conformations,
by changing some of the residue types, and by deleting some
residues, the ligand, and all the solvent molecules. It now has
an R-value of ~0.33 using all data to 1.8 Å. (You can read
more details about the model in an older rebuilding tutorial,
for the Structurally Challenged".)
- The maps (in binary CCP4 format, covering an entire unit cell):
- The WHAT_CHECK validation results file
(pdbout.txt). This report was created with
WHAT_CHECK version 20030601. A version generated on the same model,
but using a version of WHAT IF (and of course its database) dating
back to 19970813 is available here.
If you like, you can compare the two files to see if and how the
program and its database has changed, and what effects this has
for the validation of a model.
- Two O macro files that can be handy:
foreach. And a useful
user menu datablock file to read into O.
- If you can't calculate the pep-flip, rotamer side-chain fit
or real-space fit values with O, you can download the results files
- If you can't wait until you get the OOPS2 results, here are some
of the files it produces:
critique in HTML format),
mod_rebuild.notes (ditto, but
as a plain text file that you can edit as you rebuild your model
and then print and stick into your notebook),
oops.omac (the first O macro produced
by OOPS2), and
c126 (an example of an O macro for one
specific residue, in this case residue C126).
- If you're too lazy to even make your own O database, you
can download mine (binary file model.o).
Latest update at 6 October, 2006.