PDBML/XML

[Lars Skjærven]

PDB format files are not available for large structures (e.g. 4v8r. we should probably add functionality to read this at one point.

[Xinqiu Yao]

Hi,

Thanks for the note. We definitely should have it. I saw '4v8r' has used a two-letter code for the chain ID. Has it supported by PDB format? I looked over the version 3.3 but couldn't find any description.

[Lars Skjærven]

I don't think you can have two letter long chain ID in the regular PDB format - which is probably why 4v8r is not available in the old format.

It made our shiny app crash. So we need to figure out how to deal with this.

[Barry Grant]

Is the shiny PCA app online updated to the latest commits? Appears to be broken for any PDB at the minute from Align onward...

[Lars Skjærven]

Not updated for a while. Will do it later today.

[Xinqiu Yao]

I see...

Somehow, I can download the pdb by get.pdb('4v8r'), and it contains ATOM records with 'two-letter' chain IDs. Don't know why it can be there but probably reading/writing PDBML/XML is safer.

[Lars Skjærven]

Funny. at the pdb site it says "PDB format files are not available for large structures. Please use PDBx/mmCIF or PDBML/XML files." (if you try to download it.. )

Also, the coordinate file description (here: http://deposit.rcsb.org/adit/docs/pdb_atom_format.html) says that position 22 is for chain id. thus, only one letter.

[Xinqiu Yao]

This is completed with the new function read.cif(). Let me know if we should keep it open.