[Xplor-nih] Standard formats of PDB ??

[Charles at Schwieters.org]

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Hello Ramon--

> 
> Perhaps this is a stupid question, but I do wonder why
> - Xplor cannot read PDBs as provided by the protein databank?

protocol.loadPDB does a pretty good job of reading PDBs, particularly
for proteins. If you have a problem with a specific PDB entry, please
send us the ID>

> - Xplor output is not PDB standard as required for submission to the
> protein databank.
> 
> Example, an Xplor-pdb ATOM line looks like:
> 
> ATOM      7 H5'' GUA     1     305.922  17.032 -97.545  1.00  0.00
> EDHB
> 
> The last element is the segment ID.
> 
> Wheras the line for the protein databank looks like (taken from another
> PDB from the databank):
> ATOM     22 2H5*   G A   1     -12.277 -10.770   5.000  1.00  0.00
> H  
> 

PDBTool in the upcoming Xplor-NIH release has an option writeChainID,
which will write the segid to the chainID field, if it's a single
character.

best regards--
Charles
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