[Molvis-list] remediated PDB DNA cartoon display in MDL Chime

[Raymond Keller]

* Eric Martz (emartz at microbio.umass.edu) [20070916 10:29]:
> Two days ago, I noticed that FirstGlance in Jmol (version 1.0) could 
> not select DNA chains by clicking (in the "Hide.." or "Contacts.." 
> dialogs). This was a result of the changes in the remediated PDB 
> format that changed all PDB files on August 1, 2007 

Relatedly, is anyone else finding that MDL Chime is unable to
display DNA in cartoon mode?  Neither version 2.6 SP6 nor the most
recent 2.6 SP7 seem able.  It appears that pre-remediated files do
work in this regard.

For example, 1D66.  I believe these are the current, remediated
versions of 1D66, biological unit:

  http://www.pdb.org/pdb/files/1d66.pdb1.gz
  ftp://ftp.wwpdb.org/pub/pdb/data/biounit/coordinates/divided/d6/1d66.pdb1.gz

And this should be the pre-remediated version:

  ftp://ftp.rcsb.org/pub/pdb/data/biounit/coordinates/divided/d6/1d66.pdb1.gz


The remediation notes available at
http://www.wwpdb.org/documentation/format3.1-20070719.pdf, in
section 12. Nomenclature, states:
  ``Deoxy- and ribose nucleotides now have separate chemical
  definitions with the DNA forms relabeled as DA, DC, DG, DT, DI and
  DU.''

I suspect that this is what's throwing Chime off.  It looks like
nixing column 19 (the newly-added "D" characters) from DNA ATOM
records allows Chime to correctly represent DNA in cartoon style.
Such as it does.


RSK