My understanding from Gerard K is that the next version of the PDB
format will also use unjustified atom names.
Unfortunately, following mmdb, I also backed the wrong horse and assumed
space-padded atom names were here to stay. A certain amount of
re-engineering is going to be required.
My current plan (which will be implemented in clipper, but I guess mmdb
needs something similar) is to have two modes in the coordinate code: a
legacy mode which auto pads atom names on read (which is easy if the
element name is present and requires guesswork otherwise). By selecting
this mode programs will work without other modification (a 1-line change).
The new mode will auto-strip all padding from atom names. Programs which
use atom names will need to be modified (mostly find-and-replace). When
writing to a file, the atoms names will then need to be padded if and
only if the file is in traditional PDB format.
PDB files which don't have element names are going to be painful.
I can't guarantee 100% compatibility in clipper::MiniMol, so the clipper
major version will bump to 3.0.
Paul Emsley wrote:
As to the colours, that is also due, IMHO to a bug^H^H^H issue in the
mmCIF file. The atom names and elements in the mmCIF file are not
quoted so they result in simple left-hand justified strings - such as
"N" - whereas from the corresponding PDB file one would get an atom name
of " N " and an element of " N". These mmCIF simple strings don't match
Coot's (or, i imagine, many other macromolecular file-reading program's)
expectation of atom names and elements - hence it is not recognised and
is represented in grey.
