All sections

The WHAT_CHECK report is divided in two chapters, and each chapter in a series of sections. In this part of the WHAT_CHECK user course you get an overview of the content of each section.

The first chapter gives a bit of general introduction, while the second chapter is the actual report. The remainder of this web page will run parallel with those chapters and sections.


The first section is purely introductory

Some remarks regarding the output

This section gives an explanation of the categories Error, Warning, and Note that are used throughout WHAT_CHECK .

Additionally the format of residue (numbering) will be explained.

Name of PDB file

Section 1

Checks that need to be done early-on in validation

Section 2

Administrative problems that can generate validation failures

Section 3

Non-validating, descriptive output paragraph

Section 4

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Section 5

Nomenclature related problems

Section 6

Geometric checks

Section 7

Torsion-related checks

Section 8

Bump checks

Packing, accessibility and threading

Figure 39. As you can see I am working hard at this section, so come back in two weeks, and there will be more material.

Water, ion, and hydrogenbond related checks

Final summary

Suggestions for the refinement process

Residues in need of attention