[Biopython-dev] Moratorium on commits?

Morten Kjeldgaard mok at bioxray.dk
Mon Aug 12 19:42:28 UTC 2013

On 12/08/2013, at 21:25, Lenna Peterson <arklenna at gmail.com> wrote:

> * B-factor: 0.0 in permissive (code comment states this is PDB default)

The default referred to in that code comment is what the PDB annotators put in that field if the information is not provided by the depositor (which could be the case for i.e. an NMR model). From the PDB Atomic Coordinate Entry Format Description, Version 3.30:

	* If the depositor provides the data, then the isotropic B value is given for the temperature factor.
	* If there are neither isotropic B values from the depositor, nor anisotropic temperature factors in ANISOU, then the default value of 0.0 is used for the temperature factor.

In other words, the PDB format specification has no recommendations for what default values should be used if the field is blank in a malformed file, only what their staff should put in the entry when they receive it from the depositor.

So IMO Biopython is free to use None if the B-value is missing in a malformed file.

(I haven't checked the other items that Lenna mentions.)


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