<p>A PDB file is the last step in a series of operations.
For a crystal structure in very simple terms, it consists of the coordinates of the atoms placed to best fit the density map, which in turn (with these atoms due to the phase problem) is a conversion from reciprocal space which is the result of transforming the quantified dots from the pretty diffraction pattern picked up from the detector during the experiment.</p>
<blockquote>
<p>Are all these files complete in terms of the information they store?</p>
</blockquote>
<p>Not at all, a PDB file is not complete. It nearly complete when you count density in there.</p>
<blockquote>
<p>If YES, do the individual files get updated from time to time?
If YES, why/when do they get updated?</p>
</blockquote>
<p>Only, minor format upgrade, eg. <a href="https://www.rcsb.org/versions/1UBQ" rel="noreferrer">https://www.rcsb.org/versions/1UBQ</a>.
It is however very common to polish structures.
There is a tool called PDB-Redo that is commonly called in many pipelines for example to &quot;upgrade&quot; older files.
Some folk open the files in Coot and let it do its thing.
For most molecular mechanics experiments it is common to energy minimise the structure (freely, restrained by original position or restrained to density map). It is uncommon in several docking tutorials simply to keep it simple.
However, for most uses, if an aromatic ring is not quite planar or a bond is longer than most by a fraction of an Ångström, nothing happens.</p>
<p>Also worth remembering many structures are incorrect and not just imperfect: there may be actually an isopeptide bond in the core of the protein (many did go unnoticed) or an isoaspartate conversion happened or the loop is actually split due to an Asp-Pro pair autocatalysis, waters get mistaken for ligands or sidechains. If these are polished, they may get flagged as problematic, but they may be made worse.</p>

CC BY-SA 4.0
2022-02-04T10:48:54.690Z
2022-02-04T10:48:54.690Z
Matteo Ferla
<p>I know that there are thousands of PDB files stored in Protein Data Banks.</p>
<p>Are all these files complete in terms of the information they store?</p>
<p>If YES, do the individual files get updated from time to time?</p>
<p>If YES, why/when do they get updated?</p>

<pdb>
Are the information stored in the PBD files in the protein data bank complete or incomplete?
# Are the information stored in the PBD files in the protein data bank complete or incomplete?

(Asked by: username_0 on 2022-02-04)

I know that there are thousands of PDB files stored in Protein Data Banks.

Are all these files complete in terms of the information they store?

If YES, do the individual files get updated from time to time?

If YES, why/when do they get updated?

**Tags:** pdb

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## 1 answers

### Answer by username_1 on 2022-02-04. Score: 5 | Accepted answer

A PDB file is the last step in a series of operations.
For a crystal structure in very simple terms, it consists of the coordinates of the atoms placed to best fit the density map, which in turn (with these atoms due to the phase problem) is a conversion from reciprocal space which is the result of transforming the quantified dots from the pretty diffraction pattern picked up from the detector during the experiment.

> Are all these files complete in terms of the information they store?

Not at all, a PDB file is not complete. It nearly complete when you count density in there.

> If YES, do the individual files get updated from time to time?
> If YES, why/when do they get updated?

Only, minor format upgrade, eg. <https://www.rcsb.org/versions/1UBQ>.
It is however very common to polish structures.
There is a tool called PDB-Redo that is commonly called in many pipelines for example to "upgrade" older files.
Some folk open the files in Coot and let it do its thing.
For most molecular mechanics experiments it is common to energy minimise the structure (freely, restrained by original position or restrained to density map). It is uncommon in several docking tutorials simply to keep it simple.
However, for most uses, if an aromatic ring is not quite planar or a bond is longer than most by a fraction of an Ångström, nothing happens.

Also worth remembering many structures are incorrect and not just imperfect: there may be actually an isopeptide bond in the core of the protein (many did go unnoticed) or an isoaspartate conversion happened or the loop is actually split due to an Asp-Pro pair autocatalysis, waters get mistaken for ligands or sidechains. If these are polished, they may get flagged as problematic, but they may be made worse.


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