I don't think this is a PDB data quality bug, it is a PDB format feature. Every NMR PDB file contains this:
REMARK 4 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT *CRYST1* AND 1LCD REMARK 4 *SCALE* RECORDS BE INCLUDED, BUT THE VALUES ON THESE 1LCD REMARK 4 RECORDS ARE MEANINGLESS. 1LCD
At 2/26/04, Miguel Howard wrote:
Tim wrote:
> can someone duplicate/explain this? (using the latest CVS build of Jmol > on OSX.) > > launch Jmol. > load samples/1LCD. > open the script window. > enter the following commands: > > set boundbox 0.2 > color boundbox gold > set axes 0.1 > color axes dodgerblue > set unitcell 1.0 > color unitcell green > restrict none > > OMM the unitcell is at the axes origin (I couldn't see it until I > performed the restrict command). is this a bug, or...
It *is* a bug ... a data quality bug in the PDB data :-(
The relevant records in the .pdb file are: CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000
That is a lot of 1.0 values.
and the ones in the cryst1 record are showing the length of the legs of the unitcell cage in angstroms ... 1.0 angstroms :-(
Miguel
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