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 (PDF).

Hyperlinks mentioned in the chapter

1. CCP4 home page

2. Related to O:
   • O home page
   • A-to-Z of O
   • O macro pre_oops.omac. Note: if you are using an older version of O (i.e., prior to O 9.0.0), then use this version of the macro instead !

3. PDB home page

4. Related to the Uppsala Software Factory (OOPS2, MAPMAN, MOLEMAN2):
   • USF home page
   • MAPMAN manual
   • MOLEMAN2 manual
   • OOPS2 manual

5. Validation tutorial

6. Related to WHAT IF (and WHAT_CHECK):
   • WHAT IF home page
   • WHAT_CHECK home page
   • List of WHAT IF quality checks
   • Crystallographers' guide to WHAT IF validation

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).

1. 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 PDB). 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, "O for the Structurally Challenged".)

2. The maps (in binary CCP4 format, covering an entire unit cell): 2mfo_dfc.map and mfo_dfc.map.

3. 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.

4. Two O macro files that can be handy: on_startup and foreach. And a useful user menu datablock file to read into O.

5. 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 instead: pepflip.o, rsc.o, and rsfit.o.

6. If you can't wait until you get the OOPS2 results, here are some of the files it produces: mod_oops.html (residue-by-residue 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).

7. If you're too lazy to even make your own O database, you can download mine (binary file model.o).